From terryy@crl.com Fri Oct 20 02:27:31 1995 Received: from mail.crl.com for terryy@crl.com by www.ccl.net (8.6.10/950822.1) id CAA07870; Fri, 20 Oct 1995 02:13:34 -0400 Received: from crl.com (crl14.crl.com) by mail.crl.com with SMTP id AA03533 (5.65c/IDA-1.5 for ); Thu, 19 Oct 1995 23:12:09 -0700 Date: Thu, 19 Oct 1995 23:12:09 -0700 Message-Id: <199510200612.AA03533@mail.crl.com> X-Sender: terryy@mail.crl.com X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Terry Yeung Subject: Computer model for estimating reduced molecular volumes of molecules Hi, I'm looking for software that will allow me to draw a structure and calculate what the reduced molecular volume of that molecule is. Our company is on a tight budget for this software so the cheaper the better. Thanks in advance. PS: If you know of any reference tables that lists reduced molecular volumes of some organic compounds that would be of great help also. -- These words are my own and not that of Assay Technology. -- Terry Yeung Development Chemist Assay Technology Internet: terryy@crl.com From owner-chemistry@ccl.net Fri Oct 20 05:12:33 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA10180; Fri, 20 Oct 1995 05:03:50 -0400 Received: from shiva.jussieu.fr for fanny@ccr.jussieu.fr by bedrock.ccl.net (8.6.10/950822.1) id FAA12966; Fri, 20 Oct 1995 05:03:46 -0400 From: Received: from moka.ccr.jussieu.fr (moka.ccr.jussieu.fr [134.157.1.23]) by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id KAA02951 for ; Fri, 20 Oct 1995 10:02:54 +0100 Received: from [134.157.50.121] (boris.urbb.jussieu.fr [134.157.50.121]) by moka.ccr.jussieu.fr (8.6.11/jtpda-5.1) with SMTP id KAA32205 for ; Fri, 20 Oct 1995 10:02:52 +0100 Message-Id: <199510200902.KAA32205@moka.ccr.jussieu.fr> Date: Fri, 20 Oct 1995 10:04:36 +0100 To: chemistry@ccl.net Subject: bibliography Dears , Is anybody can recomand me some bibliography about Ab initio and semiempirical calculations on piperazine and substituted piperazines. Thancks for your help Fanny Bellahsene E_mail : fanny@ccr.jussieu.fr Laboratoire de pharmacochimie moleculaire Universite Paris-Diderot From owner-chemistry@ccl.net Fri Oct 20 05:22:11 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA10210; Fri, 20 Oct 1995 05:07:09 -0400 Received: from rubc.rz.ruhr-uni-bochum.de for frankrbm@rubc.rz.ruhr-uni-bochum.de by bedrock.ccl.net (8.6.10/950822.1) id FAA12969; Fri, 20 Oct 1995 05:07:04 -0400 Received: (from frankrbm@localhost) by rubc.rz.ruhr-uni-bochum.de (8.7.1/8.7.1) id KAA24112; Fri, 20 Oct 1995 10:06:44 +0100 Date: Fri, 20 Oct 1995 10:06:44 +0100 (MET) From: Robert Franke To: Marek Strajbl cc: CHEMISTRY@ccl.net Subject: Re: CCL:G:g94 manual ISBN In-Reply-To: <9510191311.aa16033@ns.karlov.mff.cuni.cz> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 19 Oct 1995, Marek Strajbl wrote: > Would someone please send me ISBN and other essential information > (author, editor etc.) for g94 manuals? > > Thanks! > Marek Strajbl > > --------------------------------- > Marek Strajbl > Institute of Physics, Charles University, Prague, CZ > e-mail: > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: owner-chemistry@ccl.net > -- Original Sender From: Address: strajbl@karlov.mff.cuni.cz > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > Michael J. Frisch Eleen Frisch James B. Forseman Gausian 94 User's Reference ISBN: 0-9636769-1-1 =================================== Michael J. Frisch Eleen Frisch James B. Forseman Gausian 94 Programmer's Reference ISBN: 09636769-2-X /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ /\ /\ /\ Robert Franke /\ /\ Fakultaet fuer Chemie /\ /\ Lehrstuhl fuer Theoretische Chemie /\ /\ Ruhr-Universitaet Bochum /\ /\ D-44780 Bochum /\ /\ Phone: 049-234-7006751 or /\ /\ 049-234-7005294 /\ /\ Fax: 049-234-7094109 /\ /\ email: Robert.Franke@rz.ruhr-uni-bochum.de /\ /\ /\ /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ From Vincent@averell.umh.ac.be Fri Oct 20 05:57:33 1995 Received: from vm1.umh.ac.be for Vincent@averell.umh.ac.be by www.ccl.net (8.6.10/950822.1) id FAA10777; Fri, 20 Oct 1995 05:51:48 -0400 From: Received: from averell.umh.ac.be by vm1.umh.ac.be (IBM VM SMTP V2R2) with TCP; Fri, 20 Oct 95 10:49:29 GMT Received: by averell.umh.ac.be (AIX 3.2/UCB 5.64/4.03) id AA29420; Fri, 20 Oct 1995 10:50:16 +0200 Message-Id: <9510200850.AA29420@averell.umh.ac.be> Subject: IR and Raman Intensities! To: chemistry@www.ccl.net (CCL-request) Date: Fri, 20 Oct 1995 10:50:16 +0100 (DFT) Cc: bouyer@ext.jussieu.fr, pavan@bnpi.com X-Mailer: ELM [version 2.4 PL0] Content-Type: text Content-Length: 3225 Here is following a summary of replies I got concerning the IR and Raman Intensities calculated in the G92 programm. The original question was : >>Could anybody explain me how are calculated >>the IR and Raman intensities in the G92 programm? >>Those intensities are expressed in km/mol and A**4/amu, >>respectively, from expression including variation of >>dipolar moment or polarisability. However I can not >>find the exact expression leading to those units. >>Could anybody help me? The responses are : > A useful reference is: > >D. J. Swanton, G. B. Backsay, and N. S. Hush, J. Chem. Phys. 84 (1986) 5715. >You might want to look at the following papers. > >Theory: >M.J.Frisch, et al. J.Chem.Phys. 84, 531(1986) >Y. Yamaguchi, et al. J.Chem.Phys. 84,2262(1986) >C. Sosa and H.B.Schlegel, J.Chem.Phys. 86,6937(1987) > >Units: >W.B. Person and D. Steele, Mol. Spectrosc. 2,357(1974) >J.Rogers and J. Hillman, J.Chem.Phys. 77,3615(1982) >K.Fox and W.B.Person, J.Chem.Phys. 64,5218(1976) >K.Kim and W.T.King, J.Chem.Phys. 80,969(1984) You can also find useful information in the book : Introduction to Molecular Spectroscopy, G. M. Barrow, International Student Edition, McGraw-Hill Book Company, Inc., New York, San Francisco, Toronto, London Kogakusha Company, Ltd. Tokyo The Chapter 4 of this book relates theoretical intensities to experimental quantities. Thanks to everibody who provide me helpful information. Have a good day. Vincent **************************************************************** * Vincent Parente * * Service de Chimie des Materiaux Nouveaux * * Center for Research in Molecular Electronics and Photonics * * University of Mons-Hainaut * * 20, Place du Parc, B-7000 Mons, BELGIUM * * e-mail : svincent@vm1.umh.ac.be * * Vincent@averell.umh.ac.be * * fax : +32 65 37 3366 * * +32 65 37 3054 * * tel : +32 65 37 3361 * **************************************************************** From owner-chemistry@ccl.net Fri Oct 20 09:57:42 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA14773; Fri, 20 Oct 1995 09:46:12 -0400 Received: from scripps.edu for rickr@scripps.edu by bedrock.ccl.net (8.6.10/950822.1) id JAA14543; Fri, 20 Oct 1995 09:46:08 -0400 Received: from aries.scripps.edu by scripps.edu (5.61/1.34) id AA07873; Fri, 20 Oct 95 06:45:36 -0700 Received: by aries.Scripps.EDU (4.1/SMI-4.1) id AA26540; Fri, 20 Oct 95 06:45:30 PDT Date: Fri, 20 Oct 95 06:45:30 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9510201345.AA26540@aries.Scripps.EDU> To: chemistry@ccl.net, neomig@charles.polymer.uakron.edu Subject: Pittsburgh_Modeling_Meeting Pittsburgh Molecular Modeling Group Meeting Friday, 11/17/95 Hosted by Professor Ken Jordan of the University of Pittsburgh Room 135, Department of Chemistry, Chevron Science Center University of Pittsburgh, Pittsburgh, PA Agenda 8:30 - 8:55 - Coffee - informal discussion 8:55 - 9:00 - Welcome - Dr. Rick Ross - PPG Industries 9:00 - 9:40 - Dr. Doug Smith - Concurrent Technologies:"Industrial Health Risk Assessment" 9:40 - 10:15 - Dr. Beverly Bendiksen - Calgon: "Scale Inhibition and Molecular Modeling" 10:15 - 10:30 - Break 10:30 - 11:05 - Prof. Ken Jordan, Dr. Sharon Frederics, Dr. Marc Pedulla - Univisity of Pittsburgh: "Properties of Water and Benzene-Water Clusters" 11:05 - 11:40 - Dr. Anne Chaka - Lubrizol: "Corrosion Mechanisms of Organopolysulfide Lubricant Additives" - Tentative 11:40 - 11:55 - Break 11:55 - 1:00 - Lunch Discussion Period - Dr. Rick Ross - PPG Industries, moderator - topics including: "Demonstrating the Value of Molecular Modeling and Bringing Modeling onto the Bench Chemists Desk - When, Where, How?" 1:00 - 1:35 - Dr. Tom Fabish - ALCOA - "Structure/Property Relationships for PCB" 1:35 - 2:25 - Dr. Doug Smith - DASGroup, Inc. - "Molecular Modeling of Polycarbonates" 2:25 - 3:15 - Closing Discussion - Open topics - Plans for next meeting. 3:15 - ? - Post - Informal Discussion Meeting is open to all interested folks. For more information contact: Rick Ross at (412) 492-5359 (Voice) or rbross@ppg.com (email) From frits@chemde4.leidenuniv.nl Thu Oct 19 07:15:25 1995 Received: from rulway.leidenuniv.nl for frits@chemde4.leidenuniv.nl by www.ccl.net (8.6.10/950822.1) id HAA10239; Thu, 19 Oct 1995 07:15:23 -0400 Received: from chemde4.LeidenUniv.nl by rulway.leidenuniv.nl with SMTP id AA01533 (5.67b/IDA-1.5 for <@RULWAY.LEIDENUNIV.NL:chemistry@www.ccl.net>); Thu, 19 Oct 1995 12:15:08 +0100 Received: by chemde4.leidenuniv.nl (920330.SGI/920502.SGI) for @RULWAY.LEIDENUNIV.NL:ubcg91v@iona.cryst.bbk.ac.uk id AA17063; Thu, 19 Oct 95 13:19:36 +0200 Date: Thu, 19 Oct 95 13:19:36 +0200 From: frits@chemde4.leidenuniv.nl (Frits Daalmans) Message-Id: <9510191119.AA17063@chemde4.leidenuniv.nl> To: Alex May Subject: Re: CCL:Routine to derive combinations of r objects chosen from among n (LONG) Cc: frits@chemde4.leidenuniv.nl, chemistry@www.ccl.net Alex May wrote: > I'm looking for an algorithm which derives combinations of r objects >chosen from among n. For instance, with 3 objects A,B and C there are 3 >combinations of pairs: AB,AC and BC. It seems to be a natural candidate >for recursion a la factorial... > > I don't want to reinvent the wheel (who does? ;-)) so does anybody have >any suggestions? Incidentally, I don't have access to all 7 volumes of >Knuth's "The art of computer programming". > > Anyhow, I'll go back to being a lurker now... > Hello, First a remark: smart of you to not re-invent the wheel. I did :-( I once made just such a routine for a regression program I was working on. You hopefully realize that, if n is big, the number of combinations grows exponentially with each r that you explore? I don't have access to Knuth's book either, but this is how I solved it: please mention the name of this re-inventer of the wheel in your program if you use it :-) 1) calculate (n over r), the binomial. Be careful to calculate it using long integer (in C), otherwise it will overflow and end up negative :-( I used this routine, it will work for n and k not too big: /* N over K = N! / (K! (N-K)! ) */ long noverk (n, k) int n; int k; { long nk = 1; int i; if ((k == 0) || (k == n)) return (nk); if (k > n / 2) k = n - k; for (i = 0; i < k; i++) nk = nk * (n - i) / (i + 1); return (nk); } This shows you how many combinations you will have to calculate, so you can print a message "come back after coffee", "come back next week" or "use a supercomputer for this" or "forget it". :-) 2) I used an array of short integers to represent the bitvector of the "objects" used: 1 means present, 0 means not present. e.g. if n = 5, k = 2 you could have vector '00101' meaning: try set {C,E} You could save some space by using a binary representation but all the fuss of getting the bits flipped is not worth it IMHO. It might be a good idea to change the algorithm so you also have rules to never try a certain object, or to always use a certain object: this is how I made the algorithm so now I have to "translate back" to the simpler version. main algorithm: setup: The first of the (n over k) bitvectors is the one with all-ones left and all-zeroes right; so (n-k)* '1', (k)* '0', '1..10..0' make a loop over the (n over k) combinations do what you want with the current bitvector in your program 3) increment the bitvector done. 3) incrementing the bitvector: I used a kind of Gray-code algorithm with the following rules: 3a) if rightmost element = '0', flip the most right occuring pattern '10' to '01' (so you must search from right to left) return (this flip is always successful) 3b) else, (this is harder) find rightmost pattern '10..01' by searching for '10' from right to left, flip the '10' to '01', and shove all '1's occuring right of this new '01' pattern to the left: in a while loop (goto loop in Fortran) flip all '01' patterns found right of the new '01' to '10'; repeat until all done. now you have a pattern of the form 'xxxxx01..10..0' return A simple example for two objects out of 4: (4 over 2) = 6 nr. bitvector 1 1100 2 1010 3 1001 4 0110 5 0101 6 0011 Enjoy, Frits Disclaimer: This algorithm is probably well-documented somewhere, so if I infringe on somebody's copyright please notify me: I do not intend to do so, I posted this message only to be of some help. It would be better if somebody posted a reference to a good review of this problem, but in my ignorance of combinatorics I know of none. This text is my own opinion, not necessarily my employer's. Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-5274505 > From frits@chemde4.leidenuniv.nl Thu Oct 19 07:19:58 1995 Hello and sorry, in my last mail the line: The first of the (n over k) bitvectors is the one with all-ones left and all-zeroes right; so (n-k)*'1', (k)*'0', '1..10..0' should of course read: (k)*'1', (n-k)*'0', '1..10..0' k^ ^n-k apologies, Frits Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-5274505 From gmercier@helix.nih.gov Fri Oct 20 10:16:33 1995 Received: from helix.nih.gov for gmercier@helix.nih.gov by www.ccl.net (8.6.10/950822.1) id KAA15927; Fri, 20 Oct 1995 10:16:32 -0400 Received: from [128.231.66.71] (ppc71.od.nih.gov [128.231.66.71]) by helix.nih.gov (8.6.12/8.6.12) with SMTP id KAA00298 for ; Fri, 20 Oct 1995 10:16:30 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Oct 1995 10:25:56 -0500 To: chemistry@www.ccl.net From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: MRI contrast media & comput. chemists? Hi! I am in the process of initiating a computational chemistry facility in the Laboratory of Diagnostic Radiology Research of the NIH. In the literature there are a few examples of molecular simulations on putative MRI contrast agents. It would be nice to identify other workers in this field with the goal of setting an informal forum for the exchange of ideas. I am aware of the NMR/MRI news group, but it is not very popular. If you are interested, please drop me a line. I will gladly share any e-mail lists, although I am in no position of reproducing the work done for the CCL :=)) Gustavo A. Mercier, Jr. M.D.-Ph.D. NIH - LDRR OD OIR LDRR Building 10 Room B1N256 10 Center Dr MSC 1074 Bethesda, Maryland 20892-1074 phone: 301-402-3586, 301-496-1981 fax: 301-402-3216 e-mail: gmercier@helix.nih.gov From gmercier@helix.nih.gov Thu Oct 19 07:28:43 1995 Received: from helix.nih.gov for gmercier@helix.nih.gov by www.ccl.net (8.6.10/950822.1) id HAA10347; Thu, 19 Oct 1995 07:28:42 -0400 Received: from [128.231.66.71] (ppc71.od.nih.gov [128.231.66.71]) by helix.nih.gov (8.6.12/8.6.12) with SMTP id HAA01561 for ; Thu, 19 Oct 1995 07:28:36 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Oct 1995 07:38:00 -0500 To: chemistry@www.ccl.net From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: MRI contrast media & comput. chemists? Status: RO Hi! I am in the process of initiating a computational chemistry facility in the Laboratory of Diagnostic Radiology Research of the NIH. In the literature there are a few examples of molecular simulations on putative MRI contrast agents. It would be nice to identify other workers in this field with the goal of setting an informal forum for the exchange of ideas. I am aware of the NMR/MRI news group, but it is not very popular. If you are interested, please drop me a line. I will gladly share any e-mail lists, although I am in no position of reproducing the work done for the CCL :=)) Gustavo A. Mercier, Jr. M.D.-Ph.D. NIH - LDRR OD OIR LDRR Building 10 Room B1N256 10 Center Dr MSC 1074 Bethesda, Maryland 20892-1074 phone: 301-402-3586, 301-496-1981 fax: 301-402-3216 e-mail: gmercier@helix.nih.gov From owner-chemistry@ccl.net Thu Oct 19 19:39:21 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id TAA03038; Thu, 19 Oct 1995 19:39:20 -0400 Received: from merit-mx1.telemail.net for Karl.F.Moschner@urlus.sprint.com by bedrock.ccl.net (8.6.10/950822.1) id TAA10075; Thu, 19 Oct 1995 19:39:18 -0400 From: X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 19 Oct 1995 19:38:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 19 Oct 1995 19:38:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 19 Oct 1995 19:38:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 19 Oct 1995 19:38:00 -0400 Date: Thu, 19 Oct 1995 19:38:00 -0400 X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Thu Oct 19 19:38:38 199500] X400-Content-Type: P2-1984 (2) Content-Identifier: Re: CCL:G:g94 ma Message-ID: <"Thu Oct 19 19:38:38 199500*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: chemistry@ccl.net, strajbl@karlov.mff.cuni.cz Subject: Re: CCL:G:g94 manual ISBN Subject: CCL:G:g94 manual ISBN Author: chemistry-request@www.ccl.net at INTERNET Date: 10/19/95 9:53 AM Would someone please send me ISBN and other essential information (author, editor etc.) for g94 manuals? Thanks! Marek Strajbl --------------------------------- Marek Strajbl Institute of Physics, Charles University, Prague, CZ e-mail: ______________________________ Reply Separator _________________________________ Michael J. Frisch, Aeleen Frisch, and James B. Foresman,"Gaussian 94 User's Reference," Gaussian Inc., 1994-1995. ISBN: 0-9636769-1-1. (Same authors), "Gaussian 94 Programmer's Reference," Gaussian Inc., 1994-1995. ISBN: 0-9636769-2-X. They also have quick refernce cards listing the options. For the latest pricing and list of additional references contact: Gaussian Inc. Carnegie Office Park, Bldg. 6 Pittsburgh, PA 15106 Phone: (412) 279-6700 FAX: (412) 279-2118 e-mail: info@gaussian.com _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ From vicpaul@ibm.net Fri Oct 20 10:14:46 1995 Received: from smtp-gw01.ca.us.ibm.net for vicpaul@ibm.net by www.ccl.net (8.6.10/950822.1) id KAA15849; Fri, 20 Oct 1995 10:14:43 -0400 From: Received: (from uucp@localhost) by smtp-gw01.ca.us.ibm.net (8.6.9/8.6.9) id OAA12178 for ; Fri, 20 Oct 1995 14:15:59 GMT Received: from slip136-68.pt.uk.ibm.net(129.37.136.68) by smtp-gw01.ca.us.ibm.net via smap (V1.3mjr) id smaKnkCrx; Fri Oct 20 14:15:15 1995 Received: by slip136-68.pt.uk.ibm.net (IBM OS/2 SENDMAIL VERSION 1.3.14/2.12um) id AA0051; Fri, 20 Oct 95 15:11:42 -0700 Message-Id: <9510202211.AA0051@slip136-68.pt.uk.ibm.net> Mime-Version: 1.0 Date: Fri, 20 Oct 95 15:04:35 +0100 To: "CCL" Reply-To: vicpaul@ibm.net Subject: Comp. Chem. in Rome Hi, I'm doing a six month consulting job with Telecom Italia on systems administration. While in Rome, I want to interact with someone at a computational chemistry group and a local university or research center. My interest/education is in Monte Carlo simulation of liquid/gas equilibrium, nucleation theory, and metastable states. If there is anyone doing any of this kind of work that would like to interact with me, drop me a line. BTW: This is not a posting for a job. I already have one. ---------------------------------------------------------------------------- V. Paul Gregory, PhD Residence Parco Solario Via Suvereto 46 00139 Roma ITALY From Jeffrey.Gosper@brunel.ac.uk Fri Oct 20 06:31:02 1995 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.10/950822.1) id GAA11600; Fri, 20 Oct 1995 06:31:00 -0400 From: Received: from loki.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <10912-0@monge.brunel.ac.uk>; Fri, 20 Oct 1995 11:30:14 +0100 Message-Id: <11152.9510201030@loki.brunel.ac.uk> Subject: M:Trying to perform IRC calculations To: chemistry@www.ccl.net Date: Fri, 20 Oct 1995 11:30:10 +0100 (BST) Dear computational chemists, I have been trying to perform an IRC calculation using MOPAC 6 (VAX/PC), however I'm having problems getting the output I require. To begin the calculation I performed the saddle calculation on the hydrogen migration of the ethyl radical as described in the MOPAC manual. I then performed a SIGMA optimization on this saddle point and ran a FORCE ISOTOPE calculation. At this stage all seems to be OK with one negative frequency corresponding to the movement of the hydrogen between the two carbons. I then performed an IRC calculation using the following keywords: UHF PRECISE IRC-1 ISTOPE RESTART as instructed in the manual (see Z-matrix). *************Z-Matrix**************** UHF PRECISE IRC=-1 isotope RESTART Ethyl radical hydrogen migration - TS C C 1.46005 1 1 H 1.08817 1 120.68855 1 2 1 H 1.08817 1 120.68851 1 157.27862 1 2 1 3 H 1.35467 1 57.39173 1 -101.36322 1 2 1 3 H 1.08817 1 120.68852 1 .00192 1 1 2 3 H 1.08817 1 120.68856 1 -157.27784 1 1 2 3 ************************************* The calculation ran without error and produced an output file which contained the internal and cartesian points, interatomic distances and the following: TIME USED UP TO RESTART = 224.95 MOLECULAR WEIGHT = 29.06 INITIAL VELOCITY IN DRC 0.04058 -0.01462 -0.07273 0.04058 0.01462 0.07273 0.01030 0.00076 -0.02641 0.01030 -0.01091 -0.02410 -1.00841 0.00000 0.00000 0.01030 -0.00077 0.02641 0.01031 0.01091 0.02409 POINT POTENTIAL + ENERGY LOST = TOTAL ERROR REF% MOVEMENT 1 62.80986 0.00000 62.80986 0.00000 1 % 0.0000 .... points removed .... 1414 10.54661 52.24357 62.79018 -0.01501 1414 % 1.6416 1415 10.54637 52.24381 62.79017 -0.01502 1415 % 1.6421 1416 10.54616 52.24400 62.79016 -0.01503 1416 % 1.6425 1417 10.54598 52.24417 62.79015 -0.01504 1417 % 1.6428 1418 10.54585 52.24430 62.79014 -0.01505 1418 % 1.6431 IRC CALCULATION COMPLETE However there is no geometries printed. I then repeated the calculation using a "T" as the bond flag for Atom 1, in order to obtain information on the turning points at the very least. However an identical output was obtained. Can anyone clarify how geometrical variables can be made to appear in the output file, or are they some place else? Thanks for you time. Jeff Gosper (Brunel) From owner-chemistry@ccl.net Fri Oct 20 11:05:08 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA16562; Fri, 20 Oct 1995 10:42:48 -0400 Received: from volta for aiba@ir.phys.chem.ethz.ch by bedrock.ccl.net (8.6.10/950822.1) id KAA15367; Fri, 20 Oct 1995 10:42:45 -0400 Date: Fri, 20 Oct 1995 15:42:29 +0100 Message-Id: <95102015422985@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) To: CHEMISTRY@ccl.net Subject: Q: diborane - ab initio and all X-VMS-To: smtp%"CHEMISTRY@ccl.net" X-VMS-Cc: AIBA Dear fellow CCLers, 1) It would be wonderful if someone could point out at the ab initio and other calculations of DIBORANE. 2) Also, the references on spectroscopical and any other experimental studies will be highly desirable. 3) But perhaps the most demanding request is this: any references to studies of the dissociation of diborane (especially in presence of other molecules as environment, for instance of helium) would be welcome ! The daunting task here is to try to submit to calculation the process of muon-minus capture by diborane and accompanying process of deborane's dissociation. Of course, the codes will be written anew - no one expects existence of standard program for this distinctly non-trivial problem. However, it's better to gather at the beginning as much information as possible. We are doing that right now and will highly appreciate help! Sincerely, Ayaz Bakasov. From patrick@hartree1.rug.ac.be Fri Oct 20 13:12:40 1995 Received: from mserv.rug.ac.be for patrick@hartree1.rug.ac.be by www.ccl.net (8.6.10/950822.1) id NAA19855; Fri, 20 Oct 1995 13:03:48 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA11861 (5.67b/IDA-1.5 for ); Fri, 20 Oct 1995 18:03:36 +0100 Received: from hartree1.rug.ac.be by allserv.rug.ac.be (5.x/SMI-SVR4) id AA06306; Fri, 20 Oct 1995 18:03:34 +0100 Date: Fri, 20 Oct 1995 18:01:35 +0200 (DFT) From: Patrick Bultinck To: CCL Subject: Bonding types in Comp. Chem. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, I have been reading quite a number of articles lately on metal-ligand interactions, energy decomposition schemes etc. Does anybody have a somewhat general review on the use of different terms to denote different bonding types in these interactions. I find it is sometimes quite hard to see things in GOOD perspective. One energy decomposition analysis defines polarization differently than another, still others speak of electrostatic interaction, while they mean ionic bond etc. (electrostatic interaction seems to be a far more general term than ionic interaction). Another traditional is polarization interaction and covalent bonding. Not seldomly do I lose perspective because every other author uses the same term, meaning something (often slightly, but importantly) different ! Also, where do I find the covalency in e.g. the Morokuma energy decomposition analysis ? There is a little part here, some there etc... Thanks for your help and/or opinions, Patrick Bultinck University of Ghent Belgium From owner-chemistry@ccl.net Fri Oct 20 14:27:40 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA21693; Fri, 20 Oct 1995 14:12:44 -0400 Received: from maroon.tc.umn.edu for harp0038@maroon.tc.umn.edu by bedrock.ccl.net (8.6.10/950822.1) id OAA17833; Fri, 20 Oct 1995 14:12:40 -0400 Received: by maroon.tc.umn.edu; Fri, 20 Oct 95 13:11:35 -0500 Date: Fri, 20 Oct 1995 13:11:31 -0500 (CDT) From: Ellsworth H Harpole Subject: nomail To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I wish to receive no mail for a while. can you help? thanks in advance. ellsworth harpole university of minnesota From C867BUC%SEMOVM.BITNET@phem3.acs.ohio-state.edu Fri Oct 20 16:12:42 1995 Received: from phem3 for C867BUC%SEMOVM.BITNET@phem3.acs.ohio-state.edu by www.ccl.net (8.6.10/950822.1) id QAA24983; Fri, 20 Oct 1995 16:09:15 -0400 Received: from SEMOVM (C867BUC@SEMOVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HWO3OMU33K95Q8HE@phem3.acs.ohio-state.edu>; Fri, 20 Oct 1995 16:08:59 EDT Date: Fri, 20 Oct 1995 13:23:08 -0600 (CST) From: "Anthony J. Duben" Subject: 1996 Summer Computer Simulation Conf To: chemistry@www.ccl.net Message-id: <20OCT95.14456615.0036.MUSIC@SEMOVM> X-Mailer: MUSIC/SP V4.1.0 Content-transfer-encoding: 7BIT Call for Papers -- 1996 Summer Computer Simulation Conference "Simulation, The Path through the Forest" July 21 - 25, 1996 Portland Hilton Portland OR sponsored by the Society for Computer Simulation You are cordially invited to participate in the 1996 Summer Computer Simulation Conference. SCSC '96 will feature contributions in all aspects of simulation and modeling related to discrete, continuous, and combined systems. Sessions will be organized to discuss current modeling and simulation practice, innovative approaches and research results. There will be contributed articles, state of the art reviews, tutorials, especially on simulation languages and environments, panels, professional development seminars, and a variety of exhibits by software vendors and publishers. SCSC '96 areas of interest include: Foundations of Simulation AI based simulation Computational Intelligence Distributed / Parallel Simulation Machine Learning Multimedia Object-Oriented Simulation Optimization Simulation Languages, Environments, and Methodologies Verification, Validation, and Accreditation Visualization and Virtual Reality Applications of Simulation Aerospace Land Vehicles Autonomous Systems and Robotics Computer Architecture Computer Systems and Networks Defense Systems Distributed Systems Environmental Applications Manufacturing Applications Physical and Chemical Sciences Engineering Applications Process Control Education and Training Applications Telecommunications Transportation Systems Submit four (4) copies of double-spaced abstracts or papers with a cover letter stating the name, address (postal and electronic), and phone and fax numbers of each author as well as the designated contact author to Society for Computer Simulation (SCSC '96) 4848 Ronson Court Suite L San Diego CA 92111-1810 Timetable: Dec 1, 1995, Two page Abstract due Feb 2, 1996, Notice of acceptance Apr 26, 1996, Camera ready manuscripts due. From mark_hanning-lee@qmail2.aero.org Fri Oct 20 17:12:42 1995 Received: from aero.org for mark_hanning-lee@qmail2.aero.org by www.ccl.net (8.6.10/950822.1) id RAA26585; Fri, 20 Oct 1995 17:06:52 -0400 Received: from qmail2.aero.org ([130.221.132.47]) by aero.org with SMTP id <111241-1>; Fri, 20 Oct 1995 14:06:09 -0700 Message-ID: Date: Fri, 20 Oct 1995 15:06:44 -0700 From: "Mark Hanning-Lee" Subject: Stirling; r objects from am To: "Compchem List" X-Mailer: Mail*Link SMTP-QM 3.0.2 Fritz Daalmans wrote: > 1) calculate (n over r), the binomial. Be careful to calculate it using > long integer (in C), otherwise it will overflow and end up negative :-( > I used this routine, it will work for n and k not too big: > /* N over K = N! / (K! (N-K)! ) */ To calculate large factorials, use the Stirling approximation. See a mathematics book like Abramowitz and Stegun. It states that log n! ~= n * log n + (other terms which I don't recall offhand) So you can estimate "n over k" without working out large factorials. If n is too large to calculate n! directly, the Stirling approximation will be very accurate. The A&S book gives many useful approximations which have been most helpful. For example you can use their approximate error function erf x to add a Gaussian distribution of noise to simulated data. Mark Dr. Mark A. Hanning-Lee | Tel: (310) 336 2835 The Aerospace Corporation | FAX: (310) 336 7680 PO Box 92957, M5-754 | Los Angeles CA 90009-2957 | Email: mark_hanning-lee@qmail2.aero.org USA From honza@zrzsp5.chem.tu-berlin.de Fri Oct 20 19:27:44 1995 Received: from mail.zrz.TU-Berlin.DE for honza@zrzsp5.chem.tu-berlin.de by www.ccl.net (8.6.10/950822.1) id TAA28830; Fri, 20 Oct 1995 19:13:07 -0400 Received: from mailgzrz.TU-Berlin.DE by mail.zrz.TU-Berlin.DE with SMTP (PP); Sat, 21 Oct 1995 00:12:40 +0100 Received: from zrzsp5.chem.tu-berlin.de by mailgzrz.TU-Berlin.DE with SMTP (PP); Sat, 21 Oct 1995 00:12:13 +0100 Date: Fri, 20 Oct 95 11:45:45 +0100 From: Jan Hrusak Message-Id: <9510201045.AA07020@zrzsp5.chem.tu-berlin.de> To: CHEMISTRY@www.ccl.net Subject: Thiazole Dear netters, I am just writing down our results on the neutral and ionic thiazole and its ylide forms. I looked up some literature databases, however, the results were not very encouradging, since I found just few entries. Uor paper deals with theoretical ab initio, DFT and HF/DFT calculations of the isolated and TM/Complexed Thiazole. I would greatly apprechiate to obtain related references in order to complete the citations. Yours Jan Hrusak J. Heyrovsky Inst. Prague CZ zrzsp5.chem.tu-berlin.de From g112976@power.ufscar.br Fri Oct 20 21:12:45 1995 Received: from fpsp.fapesp.br for g112976@power.ufscar.br by www.ccl.net (8.6.10/950822.1) id VAA00437; Fri, 20 Oct 1995 21:07:17 -0400 Received: from merak.fapesp.br by fpsp.fapesp.br with PMDF#10108; Fri, 20 Oct 1995 23:05 BDB (-0200 C) Received: from power.ufscar.br by merak.fapesp.br with PMDF#10108; Fri, 20 Oct 1995 21:30 BSC (-0300 C) Received: by power.ufscar.br (940816.SGI.8.6.9/911001.SGI) id JAA09033; Tue, 17 Oct 1995 09:41:54 -0200 Date: Tue, 17 Oct 1995 09:41:54 -0200 (BDT) From: "Augusto C. de Camargo Neto" Subject: XMol for Linux ... To: CHEMISTRY@www.ccl.net Message-id: X-Envelope-to: CHEMISTRY@www.ccl.net Content-type: TEXT/PLAIN; charset=US-ASCII MIME-Version: 1.0 Hi ... I would like to know if anyone has compiled XMol for Linux ... Thank you Augusto Camargo ----------------------------------------+--------------------------------------- | Augusto Cesar de Camargo Neto - Pateta | Keith Nelson: You can't judge a Universidade Federal de Sao Carlos | ------------- book by its cover ... Departamento de Quimica | Lab. Inter. de Eletroquimica e Ceramica | Watts: Yeah, but you can tell how Rodovia Washington Luiz, km 235 | ----- much it's gonna cost. Caixa Postal 676 - CEP 13565-905 | Sao Carlos - SP | in Some Kind of Wonderfull (1987) Brazil |--------------------------------------- | Phone: +55 16 272-6215 | John Keating: Carpe diem !!! Fax: +55 16 272-6215 | ------------ e-mail: g112976@power.ufscar.br | | in Dead Poets Society (1989) ----------------------------------------+--------------------------------------- From raman@bioc01.uthscsa.edu Fri Oct 20 21:16:21 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/950822.1) id UAA00337; Fri, 20 Oct 1995 20:59:16 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Fri, 20 Oct 1995 20:00:11 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA06170; Fri, 20 Oct 95 19:58:51 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9510210058.AA06170@bioc01.uthscsa.edu> Subject: porphyrin-protein interactions... To: chemistry@www.ccl.net Date: Fri, 20 Oct 1995 19:58:51 -0500 (CDT) X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1699 Greetings! Has anyone out there modelled porphyrin-protein interactions? I would also appreciate any citations on experimental work that deals with such interactions at the structural level. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/