From chemistry-request@ccl.net Sun Feb 20 04:51:49 2005 Received: from sungod.ccs.yorku.ca (sungod.ccs.yorku.ca [130.63.236.104]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1K9pmpT000580 for ; Sun, 20 Feb 2005 04:51:48 -0500 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.12.10/8.12.8) with ESMTP id j1K9pl9N020710 for ; Sun, 20 Feb 2005 04:51:47 -0500 (EST) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id j1K9eOY05096 for chemistry /a\ ccl.net; Sun, 20 Feb 2005 04:40:24 -0500 (EST) From: Wai-To Chan Message-Id: <200502200940.j1K9eOY05096 /a\ curl.gkcl.yorku.ca> Subject: Request: DFT methods for silica nanoparticles To: chemistry /a\ ccl.net Date: Sun, 20 Feb 2005 04:40:23 -0500 (EST) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 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 There is this method "Promolecule electron density isosurface" described in "Molecular surfaces from the promolecule: A comparison with Hartree-Fock Ab Initio electron density surfaces" Mitchell and Spackman, J comp chem, vol 21 933-92 (2000) that may perhaps suit your need. This paper reports isosurfaces of macromolecules as big a few thousand A^3. According to this paper this type of electron density isosurface is easy to calculate and compares well with results obtained from ab initio methods. Wai-To Chan <<<<<<<<<<<<<<<<<<<<<< Hello, I'm interested in simulating the detailed charge density distribution on the surface of growing silica nanoparticles (~ 3-10 nm). I'm hoping that this will be possible using DFT/pseudopotential approaches: the potential number of atoms considered in such a simulation is quite high, I know. I would be very grateful if anyone on this list could advise me on the best techniques for such simulations. I would prefer not to have to move to using empirical potentials just to make the calculation tractable. My main interest is having a reliable charge density distribution, with a view to investigations of the topology of the chage density distribution on the surface of the nanoparticles. I may also need to consider surface reconstructions and atomic substitutions in the future, so techniques that might allow a realistic model of these phenomena are also of interest to me. Any advice would be very gratefully recieved, Steve Kirk >>>>>>>>>>>>>>>> From chemistry-request@ccl.net Sat Feb 19 18:20:14 2005 Received: from exmails2.chem.ucla.edu (exmails2.chem.ucla.edu [169.232.134.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1JNKC7H011412 for ; Sat, 19 Feb 2005 18:20:13 -0500 Received: from [169.232.227.204] (ts18-191.dialup.bol.ucla.edu [169.232.227.204]) (authenticated bits=0) by exmails2.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id j1JNK8uh026338; Sat, 19 Feb 2005 15:20:10 -0800 Mime-Version: 1.0 X-Sender: scerri () chlorine.chem.ucla.edu (Unverified) Message-Id: In-Reply-To: <4ce7535b5e7449995f7e1aa1e6083c60 () cea.fr> References: <4ce7535b5e7449995f7e1aa1e6083c60 () cea.fr> Date: Sat, 19 Feb 2005 15:13:59 -0800 To: khinsen () cea.fr From: Eric Scerri Subject: Re: CCL:orbitals and reality Cc: ccl Content-Type: text/plain; charset="us-ascii" ; format="flowed" 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 In response to my recent posting shown below with double lines, >>Many useful things are unobservable! >> >>The question was indeed whether one can observe an orbital. >>I don't think anybody really doubts the usefulness of the concept. >> >>Electrons and nuclei are at least observable in principle. >>The usual understanding is that orbitals are not. Konrad Honsen responded, >Electrons and nuclei are not observable, its some of their >properties that are. The position, velocity, energy, charge, etc. >of an electron are observables. Other properties, such as its wave >function, are not observables. When we say "electrons are >observable", this is really just a shorthand for saying "electrons >have observable properties". > >Note also that the status of a quantity as an "observable" is part >of the model, not of "reality". The model of an electron with all >the properties listed in physics textbooks is the outcome of a long >process of experimentation and model making. There is no operation >that allows to establish the list of all observable properties of >an electron. They might become more numerous in the future, but >future research might also lead us to abandon the concept of the >electron, or at least downgrade its status in our understanding of >nature. ------------------------------------------------------- First an apology to those who find these continuing discussions on orbitals somewhat tedious and who wish to return to the important business of talking about the details of computational methods. To my mind this is a rather disappointing attitude. The emergence of philosophical discussions among scientists is surely a sign of change occurring and should be welcomed as a respite from the day-to-day work and as an opportunity for practitioners from different parts of the field to engage in fruitful discussion, more widely than in the normal course of events. When QM faced a crisis in the 1920s the leading physicists turned to philosophical discussion. Not that I believe that this issue will lead to a similar big breakthrough. It seems to be that there are some rather formidable grounds for believing in the real physical existence of electrons as opposed to orbitals even though neither are directly observable. Yes we only observe properties of electrons but we then infer the existence of a particle that gives rise to these properties. Starting with J.J. Thomson in 1897, if not before, many properties of electrons have been 'observed' such as its mass, charge and spin. Would it not be a miracle if all these experiments pointed towards the existence of the electron and yet there was no such particle (The no miracle argument for realism). There have been a number of very influential theories of the electron starting with Thomson, Rutherford, Bohr, Schrodinger, Dirac etc. Even though these theories may have described the electron in different ways there is little doubt about the continuity of reference. In other words there is little doubt that Thomson's electron is the same as Bohr's and Dirac's electron. In addition there has never been any feature within these theories that have specifically ruled out the physical existence of the electron. Now orbitals. By no stretch of the imagination is there the same mass of evidence for the physical existence of orbitals! Zuo et al. made a strident claim in 1999 which made the front page of Nature magazine but was duly criticized in a number of other publications. Why has it had to wait until 2005 for the first serious claim for observational evidence for orbitals (apart from Brion and other such claims of a different kind) ? Why is it that unlike in the case of electrons the theory does dictate that wavefunctions do not have a physical existence and that they are just mathematical fictions? Is it really appropriate to claim that the status of electrons vis a vis their physical existence is the same as that of atomic and molecular orbitals just because none of them are directly observable? Most philosophers of science take a realistic attitude towards electrons and other fundamental particles. Only a die-hard anti-realist like Bas van Fraassen would want to deny the existence of electrons because they cannot be observed directly. I have not taken a poll of philosophers of science on this question but I suspect that most of them would not be realists about orbitals, regardless of the recent images from Villneuve et al. Scientific realism does not rest on actually being able to observe the entity in question but is precisely a view about unobservable scientific terms and entities. It is only naive realism that requires actually observing the entity directly. regards, -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri ~~ chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://ispc.sas.upenn.edu/ From chemistry-request@ccl.net Sun Feb 20 08:19:42 2005 Received: from vreme.yubc.net (vreme.yubc.net [212.124.160.13]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1KDJepT006753 for ; Sun, 20 Feb 2005 08:19:41 -0500 Received: from vreme.yubc.net (localhost.localdomain [127.0.0.1]) by vreme.yubc.net (8.12.11/8.12.11) with ESMTP id j1JNB1Tn004407 for ; Sun, 20 Feb 2005 00:11:01 +0100 Received: (from root@localhost) by vreme.yubc.net (8.12.11/8.12.11/Submit) id j1JNB14p004405 for chemistry ~~ ccl.net; Sun, 20 Feb 2005 00:11:01 +0100 Date: Sun, 20 Feb 2005 00:11:01 +0100 From: IPSI Transactions Special Issues Message-Id: <200502192311.j1JNB14p004405 ~~ vreme.yubc.net> Subject: Call for IPSI Transactions Special Issues in 2005/6; c/ba To: chemistry ~~ ccl.net X-Spam-Status: No, hits=2.1 required=7.5 tests=COMBINED_FROM, RM_fw_FromIsPhras2 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 potential Speaker: We are pleased to inform you that both IPSI Transactions journals are planing some special issues in late 2005 and early 2006, and you are welcome to submit your paper(s), until the deadlines listed below! IPSI Transactions on Internet Research: March 31, 2005 - Special Issue on E-Education: Concepts and Infrastructure June 30, 2005 - Special Issue on E-Business: Concepts and Infrastructure IPSI Transactions on Advanced Research: March 31, 2005 - Special Issue on the Research with Multidisciplinary Elements June 30, 2005 - Special Issue on the Research with Interdisciplinary Elements Each submitted paper first undergoes the editor review, and those who pass this first stage are sent to 12 external experts for a rigorous review; decisions are made after at least 6 external reviewers respond! The review is free of charge, but the authors of the accepted papers ar expected to pay the publication fee of E400 per paper (if 4 or 5 or 6 pages of the TIR/TAR format), and the additional fee of E100 per page, for each extra page, till the maximum of 10 pages. Rigorous reviewing is the major strength of IPSI journals, which is the major contributor to their high quality! Soft copies of the existing issues of TIR and TAR can be seen at the web, and hard copies can be obtained on a special request by email, as indicated on the web, where can find all information! Sincerely yours, Prof. Dr. Veljko Milutinovic, Editor-in-Chief P.S. If you need aditional information, please reply to this e-mail.