From chemistry-request@ccl.net Sat Jan 29 05:52:36 2005 Received: from postfix1-c.free.fr (postfix1-c.free.fr [213.228.0.79]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0TAqWHj023351 for ; Sat, 29 Jan 2005 05:52:32 -0500 Received: from postfix3-1.free.fr (postfix3-1.free.fr [213.228.0.44]) by postfix1-c.free.fr (Postfix) with ESMTP id C9BD6C585DE for ; Sat, 29 Jan 2005 09:46:37 +0100 (CET) Received: from [82.66.102.10] (michelet-4-82-66-102-10.fbx.proxad.net [82.66.102.10]) by postfix3-1.free.fr (Postfix) with ESMTP id 1487F1734D9; Sat, 29 Jan 2005 09:46:37 +0100 (CET) In-Reply-To: <5.1.0.14.0.20050125110312.01ebb080:at:imap.esrf.fr> References: <5.1.0.14.0.20050125110312.01ebb080:at:imap.esrf.fr> Mime-Version: 1.0 (Apple Message framework v619) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <4951F859-71D2-11D9-B5C3-000A95AB5F10:at:laposte.net> Content-Transfer-Encoding: 7bit Cc: CCL computational chemistry list (E-mail) From: konrad.hinsen:at:laposte.net Subject: Re: CCL:[Re]: orbitals and reality Date: Sat, 29 Jan 2005 09:46:37 +0100 To: Valentina VETERE X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 25.01.2005, at 11:24, Valentina VETERE wrote: > Nevertheless, there is still something not clear in my mind. My point > is that since my first lessons on quantum mechanics I belief that all > the equations (not excluding Schrodinger or Dirac) were models of a > more complex reality that none can describe for instance with numbers. > Is this true? That's my view as well and I have had the same sense of bewilderment reading the recent discussion. For me the question is not if orbitals are "real" but if they are useful in understanding molecules. But the same comment applies to electrons and nuclei. -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen:at:cea.fr ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Sat Jan 29 01:58:41 2005 Received: from web51302.mail.yahoo.com (web51302.mail.yahoo.com [206.190.38.168]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0T6weRT016992 for ; Sat, 29 Jan 2005 01:58:40 -0500 Received: (qmail 71770 invoked by uid 60001); 29 Jan 2005 06:58:40 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=T5WqgPATHR7E8JZl2oEprpaiiDEH2CfNGZblZwBFGOijMUn6fZyQEjNtKni6geZky85O65zemIc1jXeAOz5HrBegRVgLZriqC7G93QSMZ5GschARMOEoJvud0MocVWsZ2quckFlToTyAWxPOvvDDZdlWlpAKCHYqqEBINy45Wl4= ; Message-ID: <20050129065840.71768.qmail{at}web51302.mail.yahoo.com> Received: from [24.152.170.115] by web51302.mail.yahoo.com via HTTP; Fri, 28 Jan 2005 22:58:40 PST Date: Fri, 28 Jan 2005 22:58:40 -0800 (PST) From: Sengen Sun Subject: CCL: orbitals and reality To: chemistry{at}ccl.net In-Reply-To: <7E64C424A9A62B4592CC505FD28982074A4348{at}KC-MAIL6.kc.umkc.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net First, in response to Dr. N. Sukumar s comments, I feel that the claim for the observation of HOMO in the current Nature s paper is not acceptable whatever you say. The simplest reason before anything else is that all their mathematical schemes leading to their final claim are based on their assumption that one electron has to be confined to HOMO. We all know this is not true in the reality and in the context of QM. Such an assumption leads to conceptual distortion of science. Orbitals distinguish from any physical objects. It is meaningless to compare the measurement of orbitals to any other experimental measurements. Any scientific measurements are based on well-understood physical interacting relationships between physical entities including light, or based on well-established theories. In the case of orbitals or WFs, all known theories tell us that they are not physical entities and cannot function independently. All the mathematical schemes for the WF or orbital observation are derived from our mental forces instead of any meaningful physical interaction. Consequently, a picture in human mind is obtained from forceless mathematical schemes. This is not a scientific measurement! I feel it is very critical to keep our concepts clear at this fundamental stage, or we have troubles afterward. In fact, the orbital picture they made is truly pretty. Why should I care and contest it? I was allured to this List based on my concern with the mechanism of chemical reactions. I was first noticed this 80-year old controversy from Prof. E Lewars s posting 5 years ago www.ccl.net/cgi-bin/ccl/message.cgi?2000+08+25+007 If we do have a controversy, it is not the time yet to just sing songs of triumphs. Scientists are specially needed wherever there is a controversy. If we don t care or we ignore, why should we come to science this life? I am very glad that 6 graduate students across the world contacted me for the last 4 weeks. They asked for opinions, papers, and related information. I am sure that these young people will push these scientific issues forward. What I am proud of myself is that I have brought many people s attention across the world on the interesting issues of the reaction mechanisms for the last 5 years. I have also learned something interesting from many CCL-friends. I d like to share some quotes that I have received from Internet friends: 1. Overall, I feel you have done something very interesting in the explanation of electronic reorganization mechanism. I am sure you should continue your effort in this area. 2. I think you are correct in your pursuit of a clear philosophical understanding of the use of orbitals in chemistry 3. Nice comments. Your point of view should be tought to all first year chemistry students. 4. I really admire your effort to clarify this issue. 5. The theory sounds very valuable to me. You should get them published somewhere. The quotes 1 and 5 are referring to my preprint papers: 1. Collision-induced electron reorganization as the general mechanism of concerted cycloaddition reactions. Chemistry Preprint Archive, 2001, issue 7, 199-208, ; 2. Playing the Natural Puzzles of Concerted Cycloadditions: What Are the Tricks behind the Scene? Chemistry Preprint Archive, 2002, issue 1, 49-56). __________________________________ Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. http://info.mail.yahoo.com/mail_250 From chemistry-request@ccl.net Sat Jan 29 05:38:20 2005 Received: from postfix1-c.free.fr (postfix1-c.free.fr [213.228.0.79]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0TAcIHj022939 for ; Sat, 29 Jan 2005 05:38:18 -0500 Received: from postfix3-1.free.fr (postfix3-1.free.fr [213.228.0.44]) by postfix1-c.free.fr (Postfix) with ESMTP id 97C03C59220 for ; Sat, 29 Jan 2005 09:38:36 +0100 (CET) Received: from [82.66.102.10] (michelet-4-82-66-102-10.fbx.proxad.net [82.66.102.10]) by postfix3-1.free.fr (Postfix) with ESMTP id 1549817349E; Sat, 29 Jan 2005 09:38:34 +0100 (CET) In-Reply-To: <200412100917.iBA9H0w8022295{at}apex.ibpc.fr> References: <200412100917.iBA9H0w8022295{at}apex.ibpc.fr> Mime-Version: 1.0 (Apple Message framework v619) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <29DCDFF8-71D1-11D9-B5C3-000A95AB5F10{at}cea.fr> Content-Transfer-Encoding: 7bit Cc: CHEMISTRY{at}ccl.net From: khinsen{at}cea.fr Subject: Re: CCL:Data and Knowledge Management Tools for Compuational Chemists Date: Sat, 29 Jan 2005 09:38:34 +0100 To: Marc Baaden X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 28.01.2005, at 11:37, Marc Baaden wrote: > I am looking for software, tools or general approaches to get hold of > the > wealth of information that accumulates (mostly) electronically. In > particular > emails, text/PDF/XML or similar documents, bookmarks to websites and > bibliographic references. > > The main request would be to be able to "store" information as is > without > having to enter it individually into a curated database. Filtering, > indexing > or cataloging through a script would be ok, though. A powerful search > should be possible. My main tool for information management is DEVONthink (see www.devon-technologies.com). It has a very convenient user interface for capturing information, can index PDF files, and has a very powerful search and classification system. The one thing it doesn't do is managing citations. You can throw in all the raw data (e.g. Pubmed XML) and find it back, but there is no specific support for formatting citations according to specific journals' requirements, nor for transferring them to whatever word processor you use. It's still worth throwing the files in, in particular if they contain abstracts. > Some specific points: > - concerning bibliographic references, there is a wide variety of > formats > like Pubmed, email-alerts, quotes on websites, ... sometimes with a > comment > by the person who sent the reference, sometimes with an URL link, ... > I would like to be able to gather all information in a first pass > without > having to parse the format by hand (eg where are authors, title, > etc). You can do that. > - concerning bookmarks, it would be nice to also have elimination of > duplicates > and of dead links No, not that. > - taking it one step further, indexing the sites listed in the > bookmarks might > also be an additional useful step Yes, that's possible (and very useful). > In an ideal world, I'd also love to make use of some artificial > intelligence > code (eg Self-organizing maps, textual data mining,..) or some > machine-learning > tools, but my feeling is that those are not (yet) usable by > non-experts. The DEVONthink engine is good enough to be useful, but not good enough to replace human intelligence. It can classify new data and suggest files that are similar to a given one. Major limitation: MacOS only. -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen{at}llb.saclay.cea.fr ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Sat Jan 29 13:51:25 2005 Received: from cgpsrv2.cis.mcmaster.ca (cgpsrv2.CIS.McMaster.CA [130.113.64.62]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0TIpOHj001683 for ; Sat, 29 Jan 2005 13:51:24 -0500 Received: from [24.224.150.196] (account mattacf ~~ univmail.cis.mcmaster.ca) by cgpsrv2.cis.mcmaster.ca (CommuniGate Pro WebUser 4.1.8) with HTTP id 80983606 for CHEMISTRY ~~ ccl.net; Sat, 29 Jan 2005 12:51:23 -0500 From: "Cherif Matta" Subject: CCL: orbitals and reality To: CHEMISTRY ~~ ccl.net X-Mailer: CommuniGate Pro WebUser Interface v.4.1.8 Date: Sat, 29 Jan 2005 12:51:23 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL Colleagues, I must personally thank Dr. Sengen Sun for initiating this very interesting discussion. I beleive that this is the type of discourse we should have on CCL. I m hereby adding my small contribution to this debate. I would like to draw your attention to a couple of very interesting papers by Professor Richard Bader. In these articles "Molecular Orbital Theory", which is one of the most significant pilars of chemical theory, is contrasted with "Orbitals" or "orbital models". In case you are interested, here are the references: (1) Bader R. F. W. "Letter to the editor: Quantum mechanics, or orbitals?". Int. J. Quantum Chem.; 2003, 94, 173-177. (2) Bader R. F. W., Popelier P. L. A., Keith T. A. "Theoretical definition of a functional group and the molecular orbital paradigm". Angew. Chem. Int. Ed. Engl.; 1994, 33, 620-631. Wish you all very well, Cherif ------------------------------------------------------- Cherif F. Matta, Ph.D., MCIC * Adjunct Professor of Chemistry McMaster University, Hamilton, ON, Canada. * Izaak Walton Killam Post Doctoral Fellow Department of Chemistry, Dalhousie University Halifax, NS, Canada. ------------------------------------------------------- * Web site: http://chem.utoronto.ca/~cmatta/ Tel: (902) 494 7021 Fax: (902) 494 1310 -------------------------------------------------------