From chemistry-request@ccl.net Sun Jan 23 04:34:33 2005 Received: from web51303.mail.yahoo.com (web51303.mail.yahoo.com [206.190.38.169]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0N9YVi3014177 for ; Sun, 23 Jan 2005 04:34:31 -0500 Received: (qmail 79102 invoked by uid 60001); 23 Jan 2005 08:34:29 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=MjTWnrfaCedO3AxBS7BpTOR+pWEbaqrw6QQEp/BT5Gn0m3xP9PDDnb8803pwSreNtmTimBRU/uHc+r9krCSB9gJ5KB+ICZI5etI0Mg8jksmNMqqsn5uoJNA3sDQ4MNJ6LKYqDObHCFTtzyTp2aoKmMsgVkBbaY4l90zL8M/VuD4= ; Message-ID: <20050123083429.79099.qmail)at(web51303.mail.yahoo.com> Received: from [24.152.171.220] by web51303.mail.yahoo.com via HTTP; Sun, 23 Jan 2005 00:34:29 PST Date: Sun, 23 Jan 2005 00:34:29 -0800 (PST) From: Sengen Sun Subject: CCL: orbitals and reality To: chemistry)at(ccl.net In-Reply-To: <200501180209.j0I29dk8005132)at(electra.cc.umanitoba.ca> 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 It is a wanderful discussion, better than a published paper anywhere. Thanks to every one for involvement, especially Alan Shusterman who gave an excellent, logical and fair analysis. I read each post or personal e-mail word-by-word but will not be able to reply individually. Almost all the people discuss the general philosophy on the orbital concept. But only did Phil Hultin get down to the bottom of the paper - what are the specific problems with the Nature paper (2004, 432, 867)? A realistic description of the current Nature paper should be: the authors used overtune spectrum to construct mathmatically a picture that resembles an orbital. If we use Alan's language, they built Y, and claimed it is X as Y is in the same quantum state as X. The specific problem is that they built Y based on their arbitrary pre-assumptions such as "the electrons are organized by energy in orbitals", "tunnel ionization coherently transfers a part of the bound-state electron WF to the continuum"... etc. How ridiculous are these assumptions! Can a process of electron detachment and its return back lead to any information of HOMO? How many people believe that? Do we need to know anything about their ionization technique? The magic word here is the "tunnel". I am sure the referees were scared to death by this magic word. From the first sentence to the end, authors mentally enforced their claims and did not proved them. While Louis Noodleman emphasized well the importance using orbitals in treatment of quantum systems, I could not agree more with Spanget-Larsen about the use of improper language in scientific articles. The confusion has flooded in the chemical literature for decades. We have the well-established theoretical frames of solid foundation, which says that WFs cannot be observed. Now we cannot ram these frames by exagerrating some vague experimental results. Thanks for suggestions but I don't and won't have any interest to send a paper anywhere on orbital observation. My interest is actually in interpretation of mechanisms of organic chemical reactions. There have been serious mistakes in orbital-based interpretation as I indicated earlier on the List. I formulated my own mechanistic theory of concerted cycloadditions by breaking the routine approach of IRC. For some NEW List memebers of the last two years, see my preprint papers (I will send them to you on request by personal e-mail): 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). I am better qualified to say something about the organic chemical reactions than orbital observibility. Unfortunately, I am in a direction against the main stream of the fever of MO interaction control. My papers were not welcome anywhere (partially due to my poor English), but in the chemistry preprint server, where they were once downloaded thousands of times by readers. I received several positive feedbacks from the List friends. I am confident that my papers have high scientific value but some small errors and will be recognized someday. My main idea is that chemical reactivity is decided by easiness of electron density reorganization, and the density reorganization is independent of orbital reorganization. Therefore, orbital control of chemical reactions is a conceptual mistake. My major concern with the current fundamental science is that researchers conduct too many mentally-enforced assumptions without logical physical connections. And mathematical schemes are then derived based on their mental forces. This is especially evident for the earlier claims of orbital obervations (Phys. Rev. Letters 1998, 80, 5508-5511; Nature 1999, 397, 233-235), which I criticized extensively in the PhilChem List a year ago. Mentally enforced assumptions are also a general problem in computational and theoretical chemistry. This problem has reached such a crisis that some theoreticians don't understand each other. For example, each of 3 groups (JPC A 2001, 105, 10943; 10946; 10947)enforces their own assumptions in their minds, resulting in 3 contradictory conclusions on the mechanism of a dipolar cycloaddition. Each group have their own perceptions on how (HF, Kohn-Sham, valence-bond) orbitals control electronic reorganization. There are many examples of this kind of conceptual mistakes due to the misuse of orbital. Only can my orbital-free approach in my preprint papers offer concrete evidence about electron reorganization of cycloadditions. Many authorities-controled publication media are eager for triumphs of science and even for evidently inflated ones, and have little interest to give some room for critics. This is why the CCL site is so precious to keep different thoughts exposed. I hereby appeal that the community support the CCL site financially by personal and organizational contributions. Thanks again every one. Sengen --- Phil Hultin wrote: I am getting the impression that part of the problem in this discussion is that people mean different things when they talk about "visualizing an orbital". There can be no argument that the mathematical formulation of orbital theory is a human construct, and hence that orbitals so formulated must be artificial models. These models purport to describe the spatial probability density (if that isn't a redundancy) for a single electron having a particular energy in the vicinityof a particular nucleus. Atoms apart from hydrogen have more than one electron, and our mathematical model is approximate in such cases. Therefore, it is highly probable that even if a particular application of the orbital model can give a reasonable agreement with experimental energies in the aggregate, the individual one-electron wavefunctions will not have any direct resemblance to the behaviour of any one electron in reality (whatever that may mean). On the other hand, I think it is possible (albeit not probable) that our orbital model captures some aspect of observable electronic behaviour. Thus, until someone can explain to me how Villeneuve et al's tomographic interpretation of their spectroscopic data is fundamentally wrong, I am prepared to accept that they may have visualized something real, to which our orbital model roughly corresponds. Note that I do not say that they have indeed visualized an orbital, because yes, orbitals are hypothetical objects. And, I quite agree that you cannot observe a hypothetical (or perhaps imaginary) object. So, in the strict sense there is no way that Villeneuve's claim to have observed an orbital can be correct. Is it therefore impossible to observe the spatial distribution of an electron, and for this distribution to bear some resemblance to what our theory predicts? I would welcome any reasoned and referenced rebuttal of my interpretation of Villeneuve et al's Nature paper. Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin_at_cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin __________________________________ Do you Yahoo!? Yahoo! Mail - 250MB free storage. Do more. Manage less. http://info.mail.yahoo.com/mail_250 From chemistry-request@ccl.net Sun Jan 23 01:50:57 2005 Received: from mail.iinet.net.au (mail-09.iinet.net.au [203.59.3.41]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0N6opi3026268 for ; Sun, 23 Jan 2005 01:50:53 -0500 Received: (qmail 17531 invoked from network); 23 Jan 2005 06:50:40 -0000 Received: from unknown (HELO octa4.net.au) (203.206.239.140) by mail.iinet.net.au with SMTP; 23 Jan 2005 06:50:39 -0000 Received: by octa4.net.au (sSMTP sendmail emulation); Sun, 23 Jan 2005 17:49:31 +0930 Date: Sun, 23 Jan 2005 17:49:31 +0930 From: Brian Salter-Duke To: Computational Chemistry List Subject: Re: CCL:Orbitals and Reality Message-ID: <20050123081931.GB4888..at..monster.ntu.edu.au> Reply-To: Brian Salter-Duke Mail-Followup-To: Computational Chemistry List References: <200501230004.j0N04LoK009219..at..electra.cc.umanitoba.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <200501230004.j0N04LoK009219..at..electra.cc.umanitoba.ca> User-Agent: Mutt/1.5.4i 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 On Sat, Jan 22, 2005 at 06:04:20PM -0600, Phil Hultin wrote: > I am getting the impression that part of the problem in this discussion is > that people mean different things when they talk about "visualizing an > orbital". I think it is a more fundamental difference. Here is an example I have used for many years. In a very good text book - Quantum Mechanics in Chemistry, 2nd Ed by M. W Hanna on page 189. there is Exercise 7-10:- What does the fact that the ground state of N2 is doublet-Cap sigma-g instead of doublet-Cap pi-u tell us about the ordering of the one electron MO's of nitrogen? The expected answer is that the sigma-g MO lies higher than the pi-u orbital. However, it does not. Only at miminum basis set level does the sigma-g lie higher than the pi-u. At every other MO level of theory up to the Hartree-Fock limit the opposite is true. MO theory does not predict the correct ordering of the two ion states in question. The correct answer is "Nothing at all". The fundamental conclusion to get from this is that you can not predict theory from experiment. You predict experiment from theory. In this case you find out that MO theory is not good enough at the Koopman's theory level. You have to take into account both the relaxation of the orbitals on ionisation and the effects of electron correlation. > > There can be no argument that the mathematical formulation of orbital theory > is a human construct, and hence that orbitals so formulated must be > artificial models. Indeed, but wave functions are also a human construct, but most quantum chemists think they are more fundamental than orbitals which are 1-electron functions used to approximate the N-electron molecular wave function. > These models purport to describe the spatial probability density (if that > isn't a redundancy) for a single electron having a particular energy in the > vicinityof a particular nucleus. Atoms apart from hydrogen have more than > one electron, and our mathematical model is approximate in such cases. > Therefore, it is highly probable that even if a particular application of > the orbital model can give a reasonable agreement with experimental energies > in the aggregate, the individual one-electron wavefunctions will not have > any direct resemblance to the behaviour of any one electron in reality > (whatever that may mean). Exactly > On the other hand, I think it is possible (albeit not probable) that our > orbital model captures some aspect of observable electronic behaviour. > Thus, until someone can explain to me how Villeneuve et al's tomographic > interpretation of their spectroscopic data is fundamentally wrong, I am > prepared to accept that they may have visualized something real, to which > our orbital model roughly corresponds. Yes, they probably have done this, but does the orbital model always work and more fundamentally, are they telling us about the orbital model. The orbital model comes from theory. Does this agree with experiment? In many cases, yes. In many cases, no. Experiment can not predict theory. Experiment can not tell us about orbitals. Orbitals can predict experimental results, but they may be wrong. > Note that I do not say that they have indeed visualized an orbital, because > yes, orbitals are hypothetical objects. And, I quite agree that you cannot > observe a hypothetical (or perhaps imaginary) object. So, in the strict > sense there is no way that Villeneuve's claim to have observed an orbital > can be correct. Is it therefore impossible to observe the spatial > distribution of an electron, and for this distribution to bear some > resemblance to what our theory predicts? It is clearly possible to observe an orbital in essentially a one-electron system, such as an isolated H atom. I doubt it is possible to observe the spatial distribution of an electron in N2, but one can observe, for example, the difference between N2 and N2+. Maybe that is what they are observing. Yes, orbitals are hypothetical objects, but so are exact wave functions. They are not hypothetical in the same way. The former is part of an approximate quantum mechanical description of molecules. The latter is valid for both approximations and exact solutions of the Schrodinger equation. I can see that all molecules have a wave function. I understand that orbitals are just one way of getting to that wave function. Take the James-Coolodge wave function for H2 and the improvements on this once computers could do the grunt. There is not an orbital to be seen! > I would welcome any reasoned and referenced rebuttal of my interpretation of > Villeneuve et al's Nature paper. I try to be reasoned. Cheers, Brian. > > > Dr. Philip G. Hultin > > Associate Professor of Chemistry, > > University of Manitoba > > Winnipeg, MB > > R3T 2N2 > > hultin..at..cc.umanitoba.ca > > http://umanitoba.ca/chemistry/people/hultin > > > -- Brian Salter-Duke (Brian Duke) b_duke..at..octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-92992847. http://members.iinet.net.au/~linden1/brian/ From chemistry-request@ccl.net Sun Jan 23 01:59:59 2005 Received: from mail.sysarris.soft.net (mail.sysarris.soft.net [164.164.144.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0N6xvi3026589 for >ccl.net>; Sun, 23 Jan 2005 01:59:58 -0500 Received: from RAJUV ([192.168.102.102]) (authenticated) by mail.sysarris.soft.net (8.11.2/8.11.2) with ESMTP id j0N5XaJ13741 for >ccl.net>; Sun, 23 Jan 2005 11:03:36 +0530 From: "Raju Vishwanathan" >sysarris.soft.net> To: >ccl.net> Subject: Required list of CDK2 inhibitors Date: Sun, 23 Jan 2005 10:56:46 +0530 Message-ID: <000201c5010c$21a935e0$6666a8c0<>agi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-Spam-Status: No, hits=3.2 required=7.5 tests=EXCUSE_16,NO_RDNS2 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.NETMembers I would like to have a list compounds which inhibits CDK2 receptor protein. Currently we are in the initial process of studying this group of inhibitors. Thanking you in advance. Warm Regards, Raju Vishwanathan Sr. Consultant SysArris Software # 120 A, Elephant Rock Road, III Block, Jayanagar,( Opp to HSBC ATM ). Bangalore-560011 India. Tel. No. 91-80-26654965,26655052,26642690, Fax No. 91-80-26650374 <> The information in this message is conf dential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorised. If you are not the intended recipient, any disclosure, copying, or distribution of the message, or any action or omission taken by you in reliance on it, is prohibited and may be unlawful. Please immediately contact the sender if you have received this message in error.Thank you.