From tcg@chem.unipune.ernet.in Tue Jul 1 02:49:07 1997 Received: from sangam.ncst.ernet.in for tcg@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id CAA29847; Tue, 1 Jul 1997 02:11:58 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id LAA19946 for ; Tue, 1 Jul 1997 11:48:46 +0530 (GMT+05:30) Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA29914; Tue, 1 Jul 1997 11:38:17 +0500 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.8.5/UNIPUNE-MAILHUB(02.04.97)) id LAA27533; Tue, 1 Jul 1997 11:37:24 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id LAA03100; Tue, 1 Jul 1997 11:48:40 -0500 Date: Tue, 1 Jul 1997 11:48:40 -0500 From: tcg@chem.unipune.ernet.in (Students of Dr. S.R. Gadre) Message-Id: <199707011648.LAA03100@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Dear Sirs: We are looking for the observed Hammett sigma constants for doubly substituted benzenes involving NH2, NO2, CH3, Cl, OCH3 (ortho and meta). Kindly send us these values or suggest a suitable reference. Thank you ........................Shridhar R. Gadre From jsl@virgil.ruc.dk Tue Jul 1 11:49:12 1997 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by www.ccl.net (8.8.3/950822.1) id LAA02727; Tue, 1 Jul 1997 11:46:49 -0400 (EDT) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by emma.ruc.dk (8.8.5/8.8.5) with ESMTP id RAA03063 for ; Tue, 1 Jul 1997 17:52:27 +0200 (MET DST) Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 1 Jul 97 17:44:46 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 1 Jul 97 17:44:42 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@www.ccl.net Date: Tue, 1 Jul 1997 17:44:36 +0100 Subject: CCL: CC semantics Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <20C39C6B85@virgil.ruc.dk> Buyong Ma, 23 Jun 1997: > We all know that computational chemistry is a young discipline ... I disagree. To me, computational chemistry started around 1800 with Dalton's law of multiple proportions, Gay-Lussac's law of relative volumes of reacting gases, etc. Indeed, the latter chemist stated almost two centuries ago: "We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation" (J.L. Gay-Lussac, 1808) And Charles Babbage, the "Father of the Computer": "All of chemistry, and with it crystallography, would become a branch of mathematical analysis which, like astronomy, taking its constants from observation, would enable us to predict the character of any new compound and possibly the source from which its formation might be anticipated" (Ch. Babbage, 1838) At the time of these writers computational chemistry was little more than a dream, but Babbage's vision is uncannily precise in its predictions! Evidently, the concept of computational chemistry is as old as the history of modern chemistry. Jems >--< Quotes from T J O'Donnell http://www.eecs.uic.edu/~tj/quotes.html#computational_chemistry =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757781 + 2710 Roskilde University (RUC) Fax: +45 46757721 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://frederik.ruc.dk/dis/chem/psos =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From ahocquet@tamarugo.cec.uchile.cl Tue Jul 1 16:49:14 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id QAA04026; Tue, 1 Jul 1997 16:30:58 -0400 (EDT) Received: from 146.83.5.131 ([146.83.10.67]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA16422; Tue, 1 Jul 1997 16:34:20 +0400 Date: Tue, 1 Jul 1997 16:34:20 +0400 Message-Id: <9707012034.AA16422@tamarugo.cec.uchile.cl> X-Sender: ahocquet@tamarugo.cec.uchile.cl X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: Alexandre Hocquet Subject: French computational chemistry ? Dear CClers, this message has been posted in French because of its local interest. You will find a short translation into frenglish at the end. Chers CCLeurs, Suite aux messages de semantique sur la modelisation moleculaire et la "chimie computationnelle", j'aimerais faire un petit recensement parmi les CCLeurs de France, pour savoir qui se definit comme un "computational chemist". Sauf erreur, cette expression n'existe pas en francais et la lecture recente des comptes rendus 1996 de situation des sections 16 et 17 du cnrs me laisse penser qu'il existe en France : -des chimistes theoriciens (clairement en section 17) -des biophysiciens (sections 20,21 ?), mais aucune ASSOCIATION de CHIMISTES "computationnels" (voir les definitions et la distinction avec la chimie theorique dans Reviews in Computational Chemistry, Vol 1, page vii) Si vous pensez etre plus qu'un utilisateur occasionnel des techniques de la "chimie computationnelle", mais si vous ne vous definissez ni comme un chimiste theoricien, ni comme un biophysiscien, je serais tres heureux de recevoir votre reponse . Je ferais un resume si il y a suffisament d'interet. ********************************************************************* Due to the fact that "computationnal chemistry" does not exist in the french language as it seems that no "computational chemist" community has been formed in France, i intend to make a census of whoever considers himself as a computational chemist and works in France. If you're not french but want to comment on this, you are welcome. *********************************************************************** Alexandre Hocquet Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago Centro CHILE fono : 56 2 678 45 19 fax : 56 2 696 73 59 From ahocquet@tamarugo.cec.uchile.cl Tue Jul 1 16:49:19 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id QAA04022; Tue, 1 Jul 1997 16:30:34 -0400 (EDT) Received: from 146.83.5.131 ([146.83.10.67]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA16408; Tue, 1 Jul 1997 16:33:58 +0400 Date: Tue, 1 Jul 1997 16:33:58 +0400 Message-Id: <9707012033.AA16408@tamarugo.cec.uchile.cl> X-Sender: ahocquet@tamarugo.cec.uchile.cl X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: Alexandre Hocquet Subject: semantics : a summary Dear CCLers, I have recently posted a message regarding the different possible interpretations of the expression "molecular modelling" in the CCL community. Thanks to all who replied. The answers seemed to converge on the fact that two different common interpretations may be understood (as defined in my original posting) and that the "classical methods" definition originates in that part of the "community" involved with drug design, biomolecular modelling, etc... Quite surprinsingly, the debate that followed focused on definitions of "computational chemistry", a theme that has been already discussed (again see original message). Anyway, be it computational chemistry or molecular modelling, it appears that everyone has his definition, depending on what computational chemistry (or what molecular modelling) he is involved in. Should this situation linger on, as a proof that computational chemistry is interdisciplinary , or do we need something like a iupac definition (as apparently such a thing does not exist) ? Well, i guess this is another discussion... By the way, thanks to Georg Schrekenbach for his spelling enlightment. Both spellings seem acceptable... ************************************************************************* The original message : ************************************************************************** Dear CCLers, While Boyd and Lipkowitz once intended to review definitions of "computational chemistry" (Reviews in Computational Chemistry, Vol 1, page vii), the words "molecular modelling" still appear confusing to me : While it seems logical to think that "molecular modelling" is that part of "computational chemistry" that describes behaviour of molecules by the formalism of some theoretical model, there seems to exist in the community a much more restrictive use of "molecular modelling". This second definition could be "Use of any non quantum mechanics model to describe the behaviour of molecules". If one looks at the scope of the Journal of Molecular Modeling, no semi empirical, ab initio, dft methods are quoted, while the general guidelines state that "The Journal of Molecular Modeling will cover all aspects of computational chemistry". Another example, the ICCCRE XII congress divides the scientific program in different topics. Amongst them : - Semi empirical and Ab initio quantum chemistry, dft methods - Molecular Modeling, QSAR Any hints on a proper definition ? Any historical reason for different uses of "molecular modelling" ? And, above all, one or two l ? ***************************************************************** The replies that did not appear directly in the CCL : ***************************************************************** Alexandre , In my humble opinion the term "molecular modelling" is indeed confusing at best, i think that in most circumstances the term is used where "molecular mechanics" would be better - i.e. solving classical equations of motion. (and both can be abrieviated to "MM") noj -- Dr. Noj Malcolm Theory Group, Dept. of Chemistry, University of Manchester, Oxford Road, Manchester. M13 9PL Yo estoy de acuerdo con la definicion que das antes, son tecnicas de quimica computacional que permiten simular o medelar sistemas moleculares a travez de formulismo de modelos teoricos, yo pienso que no se restringen exclusivamente a metodos no-QM, lo que pasa es que en general se atribuye el termino de modelado molecular a tecnicas usadas en biomoleculas o en macromoleculas en general, y con tal cantidad de atomos quedan descartado los metodos de QM, si se quieres analizar todo esa macromolecula... en todo caso hay varios trabajos que mezclan tenicas de dinamica molecular y de QM, primero estudiando las conformaciones de la macromolecula con DM y luego en un entorno mas especifico, el sitio activo (con mucho menos atomos), con QM. La otra tecnica que creo que ha cobrado gran interes son los metodos hibridos QM/MM, en dosnde se definen zonas QM y zonas MM, se mezclan los Hamiltonianos de las zonas QM con los Potenciales de MM, y "ojo" que no se tienen malos resultados en cuanto a calculos de delta G, y otras energias. En resumen, el molecular modelling, a mi juicio, no esta restringido estrictamente a metodos no-QM, sino que a todos los metodos para simulacion de sistemas macromoleculares, especilemente de interes biologico, tal vez por la estrecha relacion que existe entre molecular modelling y "molecular desing", de gran interes en la industrias Farmaceuticas Espero que te ayuda en algo esto, nos vemos en algun congreso! Danilo Gonzalez. Universidad de Santiago de Chile Facultad de Quimica y Biologia http://quimbio.usach.cl/~danilo/ Hi Alexandre, this sounds like an interesting question so a summary in the CCL would be appreciated. I have seen both of your definitions with the second one being more often used (to increase confusion, you can also add "simulation" vs. "modelling" ...). One more little comment >And, above all, one or two l ? My dictionary (Langenscheidt English - German) doesn't contain "model(l)ing", however, for "model(l)er" both one and two l are offered without any preference. Regards, Georg You raise an interesting point. > Any hints on a proper definition ? For some reason, "molecular modeling" is usually used to encompass non-quantum-mechanical treatments of chemical structures. In common usage, it tends to refer to molecular mechanics as well as pure visualization, and to things "in between", such as rule-based methods for docking and hand-manipulation of structures, generally on a computer. I really don't have any good idea why or how the term got to include these things and to exclude others, nor am I aware of any formal definition. Like your original comments, my sense of how the word is used is based on how I've seen the term used -- not on any formal definition I've seen. -P. -- **** "Deep Blue can't triumph in the game of life." (NY Times, 5/13/97) *** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * Alexandre Hocquet Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago Centro CHILE fono : 56 2 678 45 19 fax : 56 2 696 73 59 From wipke@SECS.UCSC.EDU Tue Jul 1 21:49:15 1997 Received: from MOLENG.UCSC.EDU for wipke@SECS.UCSC.EDU by www.ccl.net (8.8.3/950822.1) id VAA04976; Tue, 1 Jul 1997 21:40:41 -0400 (EDT) Received: by SECS.UCSC.EDU (MX V3.1C) id 13148; Tue, 01 Jul 1997 18:40:33 PDT Date: Tue, 01 Jul 1997 18:40:31 PDT From: "W. Todd Wipke" To: chemistry@www.ccl.net Message-ID: <009B69D6.B7E63F3C.13148@SECS.UCSC.EDU> Subject: Postdoctoral Fellowship Available Molecular Engineering Laboratory Department of Chemistry University of California Santa Cruz CA 95064 Two postdoctoral fellowships are immediately available in molecular modeling and automated de novo design of molecular structures. The research requires knowledge of C and program development, as well as the ability to work as part of a development team. Experience with Discover/Insight is also desired. Our research is aimed at developing methods for automating the precision design of molecular structures for drugs, new materials, and nanotechnology. We have applied our methodology, INVENTON, to the design of candidates targeted against a specific cancer mechanism, our collaborators then are synthesizing and testing the compounds. Candidates for these positions should send their curriculum vitae and references to Professor Todd Wipke at the above address, or by email to wipke@moleng.ucsc.edu, or by fax to 408-459-2935 (address it to Wipke). [Santa Cruz is 80 miles south of San Francisco, 35 miles from Silicon Valley, and directly on silicon beach, across the bay from Monterey.]