From jsl@virgil.ruc.dk Mon Jun 30 08:03:15 1997 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by www.ccl.net (8.8.3/950822.1) id HAA23305; Mon, 30 Jun 1997 07:39:25 -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 NAA12703 for ; Mon, 30 Jun 1997 13:44:51 +0200 (MET DST) Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 30 Jun 97 13:37:11 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 30 Jun 97 13:37:01 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@www.ccl.net Date: Mon, 30 Jun 1997 13:36:55 +0100 Subject: CCL:CC semantics Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <4A1FC4B38@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 ophira@keyscan.com Mon Jun 30 08:48:58 1997 Received: from mailnfs0.tiac.net for ophira@keyscan.com by www.ccl.net (8.8.3/950822.1) id IAA23670; Mon, 30 Jun 1997 08:38:29 -0400 (EDT) Received: from keyscan.tiac.net (keyscan.tiac.net [199.3.128.220]) by mailnfs0.tiac.net (8.8.0/) with SMTP id IAA24902 for ; Mon, 30 Jun 1997 08:38:28 -0400 (EDT) Received: by keyscan.tiac.net with Microsoft Mail id <01BC8531.202F6540@keyscan.tiac.net>; Mon, 30 Jun 1997 08:39:29 -0400 Message-ID: <01BC8531.202F6540@keyscan.tiac.net> From: OPHIRA AHARONSON To: "'chemistry@www.ccl.net'" Subject: unsubscribe Date: Mon, 30 Jun 1997 08:39:24 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit unsubscribe From gostowskir@apsu01.apsu.edu Mon Jun 30 08:49:02 1997 Received: from apsu02.apsu.edu for gostowskir@apsu01.apsu.edu by www.ccl.net (8.8.3/950822.1) id IAA23569; Mon, 30 Jun 1997 08:19:59 -0400 (EDT) Received: from gostowskir.apsu.edu by APSU02.APSU.EDU (PMDF V5.1-4 #16785) with ESMTP id <01IKOBJNMT5S0000VI@APSU02.APSU.EDU> for chemistry@www.ccl.net; Mon, 30 Jun 1997 07:18:27 CST Date: Mon, 30 Jun 1997 07:19:59 -0500 From: Rudy Gostowski Subject: molecular dynamics of anisotropic free radicals To: CCL group Message-id: <01IKOBJNNBN60000VI@APSU02.APSU.EDU> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1155 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal CCL Group, I would like to do molecular dynamics calculations of anisotropic free radicals combining in a bimolecular fashion to form dimers. The reactants are sterically hindered carbon free radicals. Please suggest references and programs. I have read Solc & Stockmayer (1971). thanks, Rudy Rudy Gostowski Department of Chemistry Austin Peay State University Box 4547 Clarksville, TN 37044 615-648-7624 FAX 615-648-5996 gostowskir@apsu01.apsu.edu From lestaw.k.bieniasz@uni-tuebingen.de Mon Jun 30 10:53:26 1997 Received: from outmail.zdv.uni-tuebingen.de for lestaw.k.bieniasz@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id KAA24951; Mon, 30 Jun 1997 10:42:56 -0400 (EDT) Received: from echem5.orgchemie.chemie (echem5.orgchemie.chemie.uni-tuebingen.de) by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA00897; Mon, 30 Jun 97 16:42:32 MES Date: Mon, 30 Jun 1997 16:42:03 +0200 (W. Europe Daylight Time) From: "Lestaw K. Bieniasz" To: chemistry@www.ccl.net Subject: Re: CCL:CC semantics/reply to Bieniasz Message-Id: X-X-Sender: coibi01@mailserv.uni-tuebingen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tuebingen, 27.06.97 Dear Dr. Yadav, Well, I may be right or wrong, or most likely the truth lies in-between. Anyway, I understand from your arguments that you belong to this group of scientists who prefer to place strong dividing lines between various scientific disciplines (you view computers and computations as nothing but tools to solve chemical problems). This is exactly opposite to the point of view I am trying to develop, since I would prefer to remove the artificial borders between the traditional scientific disciplines. Let me ask a question: If somebody elaborates a purely numerical algorithm of solving a particular type of a Schroedinger equation, that makes sense only in some chemical context, so that the method is not likely to be used outside, is he doing chemistry or computer science? Is he merely creating a new tool, or improving the chemical knowledge/methodology? (Is a methodology of solving problems in a scientific discipline a part of this discipline, or it's a quite separate matter?) If you say that it is only tool, then why do you actually see a need for "computational chemistry"? Wouldn't it be easier to say that there is only "chemistry" and that some people use computers as tools to solve chemical problems? But if you see a need for "computational chemistry", then isn't it perhaps that some new quality is created by joining the two fields (chemistry and computational science) together, that is not contained in none of the two areas separately? If so, then maybe you should not classify computers and computational methods merely as tools? What is a difference between computer modelling and simulation? I would agree to using both of them, and I doubt if there exist a single definition of "simulation" that would satisfy everybody. There was quite a funny article about this in one of early volumes of the journal called "Simulation" about 10-15 years ago. The name of the author was Fritz, as far as I remember (but I can be wrong), I would recommend this article to you and to everybody who likes to use the term "simulation" ... Best regards, L. Bieniasz *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *-------------------------------------------------------------------* From lestaw.k.bieniasz@uni-tuebingen.de Mon Jun 30 10:53:36 1997 Received: from outmail.zdv.uni-tuebingen.de for lestaw.k.bieniasz@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id KAA24924; Mon, 30 Jun 1997 10:42:14 -0400 (EDT) Received: from echem5.orgchemie.chemie (echem5.orgchemie.chemie.uni-tuebingen.de) by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA00890; Mon, 30 Jun 97 16:41:46 MES Date: Mon, 30 Jun 1997 16:41:19 +0200 (W. Europe Daylight Time) From: "Lestaw K. Bieniasz" To: chemistry@www.ccl.net Subject: Re: CCL:CC semantics Message-Id: X-X-Sender: coibi01@mailserv.uni-tuebingen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tuebingen, 27.06.97 Dear Dr. Buyong Ma, Yes, you're right I posted that letter a couple of months ago, but there were not too many responses. (Nevertheless, I wish to thank to those who responded). My personal point of view (unfortunately not shared with the scientific establishment) is that we should not pay too much attention to the classification of scientific activities. It should not really matter whether somebody is doing chemistry or physics or physical chemistry, etc. The only thing that matters should be the quality of the research. I wish we all could say "we do science", instead of trying hard to specify which particular part of it we do. I am sure this attitude would bring more progress into science, since it would allow the individuals to freely cross the real or imaginary borders between various research areas. This way of looking at science would also remove some of the semantic difficulties that you mention. But of course this is an idealistic dream, since in reality everything in science is divided into disciplines, and this system is very conservative, although as you rightly point out, there is a lot of overlapping between the disciplines (often viewed as uncomfortable). Now, since it looks that we indeed have to live in this reality, then my suggestion simply is that we use right words to denote things. Thus, in my opinion the term "computational chemistry" should be used to denote what it (literally) means. And it certainly means a combination of chemistry and computations, without specifying whether the subject is molecular or not. This understanding of computational chemistry is in a certain contrast to the current practice, in which the term "computational chemistry" is often interpreted in a much narrower sense, so that if my suggestion is accepted, it would indeed mean a certain enlargement of the scope of the (currently understood) computational chemistry. Note, however, that I have not invented this "new" definition, because it is already contained in one of the volumes of "Reviews in Computational Chemistry" ! In the same spirit, I think that the term "molecular modelling" should be used to denote any kind of modelling in which the assumed molecular structure of matter plays a central role, independently of whether the modelling is computational or not, although in practice it will of course be mostly computational, because non-computational methods are of limited use here. With best regards, Yours sincerely, L.Bieniasz *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *-------------------------------------------------------------------* From rahsjc@rohmhaas.com Mon Jun 30 16:49:02 1997 Received: from nmho05u.rohmhaas.com for rahsjc@rohmhaas.com by www.ccl.net (8.8.3/950822.1) id QAA27784; Mon, 30 Jun 1997 16:33:02 -0400 (EDT) Received: by nmho05u.rohmhaas.com; id QAA29722; Mon, 30 Jun 1997 16:47:23 -0400 (EDT) Received: from fermi.sh.rohmhaas.com(136.141.248.15) by nmho05u.rohmhaas.com via smap (V3.1.1) id xma029644; Mon, 30 Jun 97 16:47:06 -0400 Received: from localhost (rahsjc@localhost) by fermi.sh.rohmhaas.com (AIX4.2/UCB 8.7/8.7) with SMTP id QAA44340; Mon, 30 Jun 1997 16:33:00 -0400 (EDT) X-Authentication-Warning: fermi.sh.rohmhaas.com: rahsjc owned process doing -bs Date: Mon, 30 Jun 1997 16:33:00 -0400 (EDT) From: "Subhas J. Chakravorty" X-Sender: rahsjc@fermi.sh.rohmhaas.com To: Shubin Liu cc: chemistry Subject: Re: CCL:calculate exchange energy from Hartree-Fock wavefunction In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The definition of exchange energy in the Roothaan Hartree Fock method (Open Shell is a multideterminantal wavefunction) is "unambiguosly:" defined As V(Ex)= Vee - Vcoul. V(coul) = 1/2 Integral [ (rho(1) Rho(2) ] Dt1 Dt2 if Lowdin definition that Hartree Fock doesnt contain correlation energy is used. Most of the coupling coeeficients are made so that only K survives At least in Prof. Gulzari Malli's tables. The other choice is to unravel Sasaki's code or look at Froese Fischers program. Therefore the Exchange energy contains, a little correlation energy implicit in the ROHF wavefunction for open shells. With an ROHF wavefunction it is hard to seperate Exchange and correlation. just as we cant in a CI wavefunction. ********************************************* In some cases though one can construct a single determinantal function for an open shell case using the ROHF orbitals. Then calculate using the UHF equations to determine exchange, since the total energy for the UHF and the ROHF is the same, only the UHF energy need not be at a minimum with the ROHF orbitals. ByeBye. On Mon, 30 Jun 1997, Shubin Liu wrote: > > Hi, All: > > I recently hope to calculate explicitly the exchange energy of atoms from > the restricted Hartree-Fock wavefunction of Clementi and Roetti. I > obtained the right answer from atoms with 1s and 2s orbitals, but found > something wrong for those with 2p or other orbitals. I guess it may be > related to my incorrect treatment of spherical harmonic polynomials when > l>=1. Can anyone point out how to do that? Thank a lot! > > Shubin > ............................................................................. Subhas J. Chakravorty, sjchakravorty@rohmhaas.com (215)-619-5481 Rohm and Haas Company Spring House, PA-19447 ************************************************************************** Disclaimer : Opinions in the above text are not of Rohm and Haas Company + ************************************************************************** From ahocquet@tamarugo.cec.uchile.cl Mon Jun 30 18:49:02 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id SAA28762; Mon, 30 Jun 1997 18:25:16 -0400 (EDT) Received: from [146.83.10.67] by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AB08407; Mon, 30 Jun 1997 18:27:55 +0400 Date: Mon, 30 Jun 1997 18:27:55 +0400 Message-Id: <9706302227.AB08407@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 Mon Jun 30 18:49:08 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id SAA28759; Mon, 30 Jun 1997 18:24:53 -0400 (EDT) Received: from 146.83.5.131 ([146.83.10.67]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA08407; Mon, 30 Jun 1997 18:27:52 +0400 Date: Mon, 30 Jun 1997 18:27:52 +0400 Message-Id: <9706302227.AA08407@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