From owner-chemistry@ccl.net Sun Dec 11 01:00:00 2005 From: "Avijit Ghosh avijit~!~physics.drexel.edu" To: CCL Subject: CCL: Advice to Prof. Avijit Ghosh Message-Id: <-30271-051211004254-10071-5EyOrwSab3Xz7iijV9k+mw_+_server.ccl.net> X-Original-From: Avijit Ghosh Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sun, 11 Dec 2005 00:42:42 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Avijit Ghosh [avijit/./physics.drexel.edu] > Professor Ghosh arbitrarily fabricated and distorted > the history by saying : [] I did not mean to arbitrarily fabricate and distort history by adding that addendum and I apologize for doing so. I found it amusing because I seem to recall getting into a debate on a variation of the theme back in the day (w/ Dr. Scerri as I recall) and found it interesting that the issue hadn't been resolved satisfactorily at this point to anyones mind and moreover has become somewhat of a perennial staple on CCL. All the best in your research endevours. -avi _____________________________________________________________________ Avijit Ghosh, Ph.D. Drexel University, Dept of Physics Asst. Professor 3141 Chestnut st Phone: 215-895-2726 Philadelphia, PA 19104 Fax: 215-895-5934 Web: http://bio.physics.drexel.edu From owner-chemistry@ccl.net Sun Dec 11 04:42:00 2005 From: "makowskm-x-chemia.uj.edu.pl" To: CCL Subject: CCL: Orbitals and Philosophy Message-Id: <-30272-051211044000-28424-2ArmIxMqLF0rLFlhs6YDNA#server.ccl.net> X-Original-From: makowskm]_[chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-2 Date: Sun, 11 Dec 2005 10:39:51 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: makowskm,,chemia.uj.edu.pl > Sent to CCL by: Avijit Ghosh [avijit{=}physics.drexel.edu] > > That said I *personally* think orbitals are real in the same sense the > multielectronic eigenstates are real for a system. > > That is if we neglect e-e-, interactions, we get orbitals. > > It seems to me that in the same sense any statement of *electronic* > observables is in essense a "model" that are actually strictly > non-observable due to the fact the observability in QM is based on > making the born-oppenheimer approximation neglecting e-/nuclear > interactions. > > To put it into two sentences: > > If we are comfortable neglecting e-e- interactions, everything becomes > hydrogeneic -> hense orbitals. > > If we are comfortable neglecting nuclear,e- interactions ala > born-oppenheimer, we can do quantum mechanics on electrons only -> hense > multi-electron eigenstates and energy eigenvalues. > I cannot agree with any of these statements, and think that they are rather misleading then having any value for this discussion. First, I do not think you can put multielectron eigenstates and orbitals at the same level of approximation. Multielectron wavefunction is some more or less valid description of reality, as refers to the real multi-electron system; orbitals are in the best only blocks to build this description, not having a chance to describe a system as a whole by itself. The only exception to this when your statement would be valid are one-electron systems or systems where e-e interaction might be ignored. Such systems rarely are of interest for chemists. Another point is you cannot say that neglecting e-e interaction and Born-Oppenheimer approximation are approximations of comparable origin and validity. BO approximation does not neglect n-e interactions, but assumes only that nucleus are infinitibly heavy compared to electrons, which is far more reasonable and useful (in the sense of generating good model) then neglecting electrostatic interaction either n-e or e-e type. Yours, Marcin Makowski -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm_._chemia.uj.edu.pl or Kyushu University email:marcin_._cube.kyushu-u.ac.jp From owner-chemistry@ccl.net Sun Dec 11 10:56:01 2005 From: "Eric Scerri scerri ~~ chem.ucla.edu" To: CCL Subject: CCL: Advice to Prof. Avijit Ghosh Message-Id: <-30273-051211020441-5560-dy/YMzUo1WZFWld2orMTWA,,server.ccl.net> X-Original-From: Eric Scerri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Sat, 10 Dec 2005 23:00:26 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Eric Scerri [scerri*o*chem.ucla.edu] Actually the issue has moved on at least as far as I am concerned. I am more interested in understanding the claims made by the experimenters regarding the detection of phases than in the previous are they real/observable business. I tried to make that clear in my last posting. eric scerri On Dec 10, 2005, at 10:02 PM, Avijit Ghosh avijit~! ~physics.drexel.edu wrote: > Sent to CCL by: Avijit Ghosh [avijit/./physics.drexel.edu] > >> Professor Ghosh arbitrarily fabricated and distorted >> the history by saying : [] > > > I did not mean to arbitrarily fabricate and distort > history by adding that addendum and I apologize for doing so. I > found it > amusing because I seem to recall getting into a debate on a > variation of > the theme back in the day (w/ Dr. Scerri as I recall) and found it > interesting that the issue hadn't been resolved satisfactorily at > this > point to anyones mind and moreover has become somewhat of a perennial > staple on CCL. > > All the best in your research endevours. > > -avi > > _____________________________________________________________________ > Avijit Ghosh, Ph.D. Drexel University, Dept of Physics > Asst. Professor 3141 Chestnut st > Phone: 215-895-2726 Philadelphia, PA 19104 > Fax: 215-895-5934 Web: http://bio.physics.drexel.edu > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > Dr. Eric Scerri Department of Chemistry & Biochemistry, Charles Young Drive, Los Angeles, CA 90095. 310 206 7443 fax: 310 206 2061 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://springerlink.metapress.com/(uw25gnu4jydrz5555tyeokjs)/app/home/ journal.asp?referrer=parent&backto=linkingpublicationresults,1:103024,1 From owner-chemistry@ccl.net Sun Dec 11 12:50:00 2005 From: "Dr. N. SUKUMAR nagams---rpi.edu" To: CCL Subject: CCL: Orbitals and Philosophy Message-Id: <-30274-051211112703-5444-ngohC6k91GvMtBQWpl00pQ(-)server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Sun, 11 Dec 2005 11:26:58 -0500 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams*|*rpi.edu] ==============Original message text=============== On Sun, 11 Dec 2005 4:50:59 EST "makowskm-x-chemia.uj.edu.pl" wrote: Sent to CCL by: makowskm,,chemia.uj.edu.pl First, I do not think you can put multielectron eigenstates and orbitals at the same level of approximation. Multielectron wavefunction is some more or less valid description of reality, as refers to the real multi-electron system; orbitals are in the best only blocks to build this description, not having a chance to describe a system as a whole by itself. The only exception to this when your statement would be valid are one-electron systems or systems where e-e interaction might be ignored. Such systems rarely are of interest for chemists. Another point is you cannot say that neglecting e-e interaction and Born-Oppenheimer approximation are approximations of comparable origin and validity. BO approximation does not neglect n-e interactions, but assumes only that nucleus are infinitibly heavy compared to electrons, which is far more reasonable and useful (in the sense of generating good model) then neglecting electrostatic interaction either n-e or e-e type. Yours, Marcin Makowski -- ===========End of original message text=========== While this reasoning is valid for hydrogenic orbitals, it does not hold for Hartree-Fock, Kohn-Sham, natural orbitals, etc. Thus Hartree-Fock orbitals DO include an effective electron-electron interaction at the mean field level. Neglecting inter-electron CORRELATION is an approximation at roughly the same level as the others mentioned, including B-O. Note also that the usual (m/M)^1/4 perturbative treatment of Born and Oppenheimer (1927) hides some of the physics of the problem, as was elaborated by Max Born himself in 1951 (Nachr.Akad.Wiss.Goettingen). While nucleii are always a factor of a thousand heavier than electrons, there are many situations (conical intersections, avoided crossings) where B-O is not even approximately valid. Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From owner-chemistry@ccl.net Sun Dec 11 13:24:01 2005 From: "Cesar Millan pachequin(-)gmail.com" To: CCL Subject: CCL: Free Molecular Protein And Nucleic Acid Software Message-Id: <-30275-051211121822-23251-JNfsBtS0GKXNRP8Fscb4Qg**server.ccl.net> X-Original-From: "Cesar Millan" Sent to CCL by: "Cesar Millan" [pachequin]~[gmail.com] Hello everyone! I want to mutate protein residues or nucleic acid bases and I'm looking for free software that could do this from a DNA-Protein complex. One remarkable point is that the software must preserve the geometrical parameters of the DNA bases, is that possible? Thank you for any suggestion. Cesar From owner-chemistry@ccl.net Sun Dec 11 13:59:01 2005 From: "Avijit Ghosh avijit(~)physics.drexel.edu" To: CCL Subject: CCL: Orbitals and Philosophy Message-Id: <-30276-051211110731-27035-piykOJtsBSEvUnTAOR6EuQ:server.ccl.net> X-Original-From: Avijit Ghosh Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sun, 11 Dec 2005 11:06:58 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Avijit Ghosh [avijit|physics.drexel.edu] Dr. Makowski wrote: > I cannot agree with any of these statements, and think that they are > rather misleading > then having any value for this discussion. Well all right then. > First, I do not think you can put multielectron > eigenstates and orbitals at the same level of approximation. I am not saying that they are the *same level* of approximation. I am saying that they are both *a* level of approximation. Whether they are a *good enough* approximation depends on the application that you are looking at and who is doing the looking. Multielectron > wavefunction > is some more or less valid description of reality, as refers to the real > multi-electron system; orbitals are inthe > best only blocks to build this description, not having a chance to > describe a system as a whole by itself. But I could counter and say that the multielectron wavefunction are the building blocks for a electronic/nuclear wave function not having the chance to describe system as a whole by itself where *I* have defined the system to include the proper treatment of the nuclei and the electrons. > The only exception to this when your statement would be valid are > one-electron systems or systems > where e-e interaction might be ignored. Such systems rarely are of > interest for chemists. > Another point is you cannot say that neglecting e-e interaction and > Born-Oppenheimer approximation are > approximations of comparable origin and validity. BO approximation does > not neglect n-e interactions, > but assumes only that nucleus are infinitibly heavy compared to electrons, > which is far more reasonable and > useful (in the sense of generating good model) then neglecting > electrostatic interaction either n-e or e-e type. You are of course correct, I did not mean to imply that all e-/nuclear interactions are being neglected in totality but that the context of wavefunctions that the wavefunction of the system is treated as purely an electronic wave function (w/ a classical coulombs law interaction w/ a stationary nucleus) ignoring the fact that properly treated wavefunction for chemical systems would be treated as psi(e-,nuclei). I also agree that that BO is a more useful approximation than "orbitals" especially for quantum chemists. But I have been under the impression this discussion has never been about utility (which depends on the people doing the utilizing) but "reality". That is no one has ever asked whether "orbitals" are "useful" so much as whether they are "real". After all if the utility argument is being used one would have to insert for pedagogical reasons into textbooks the statement "orbitals are not real for chemists" or "orbitals are not real for quantum chemists" or even "orbitals are not as real as other non-real approximations". _____________________________________________________________________ Avijit Ghosh, Ph.D. Drexel University, Dept of Physics Asst. Professor 3141 Chestnut st Phone: 215-895-2726 Philadelphia, PA 19104 Fax: 215-895-5934 Web: http://bio.physics.drexel.edu From owner-chemistry@ccl.net Sun Dec 11 20:48:01 2005 From: "makowskm[*]chemia.uj.edu.pl" To: CCL Subject: CCL: Orbitals and Philosophy Message-Id: <-30277-051211204555-11918-0aIcy8BCDjCpfpE0JeUA6A..server.ccl.net> X-Original-From: makowskm[a]chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-2 Date: Mon, 12 Dec 2005 02:45:49 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: makowskm#%#chemia.uj.edu.pl > While this reasoning is valid for hydrogenic orbitals, it does not hold > for Hartree-Fock, Kohn-Sham, natural orbitals, etc. Thus Hartree-Fock > orbitals DO include an effective electron-electron interaction at the > mean field level. Neglecting inter-electron CORRELATION is an > approximation at roughly the same level as the others mentioned, > including B-O. Note also that the usual (m/M)^1/4 perturbative treatment > of Born and Oppenheimer (1927) hides some of the physics of the problem, > as was elaborated by Max Born himself in 1951 > (Nachr.Akad.Wiss.Goettingen). While nucleii are always a factor of a > thousand heavier than electrons, there are many situations (conical > intersections, avoided crossings) where B-O is not even approximately > valid. > > Dr. N. Sukumar > Center for Biotechnology and Interdisciplinary Studies > Rensselaer Polytechnic Institute Dear Dr Sukumar, 1. I am aware that HF approximation does not neglect e-e interaction but coulombic correlation only, but I was just discussing the point rised by Prof. Ghosh. 2. Yes, this is true that BO approximation is not always really good, I myself work a lot in the area of vibronic coupling. 3. Above two does not change the fact that steps taken going down from nuclear+multi-electron to multi-electron and from multi-electron to single electron description are qualitatively different. Full nuclear and electron wavefunction might be written as product of nuclear and multi-electron functions when vibronic coupling is neglected. This is not the case when you forget about the electron(coulombic) correlation and go to orbital approximation. Total electron wavefunction is not a product of one-electron orbitals - if you want to have it this way you miss exchange. This argument still holds true for Kohn-Sham, but here the story is even worse - orbitals does not even try to represent any real system - they are just used to generate density and recover kinetic energy in an easy way. Yours, Marcin Makowski -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm+*+chemia.uj.edu.pl or Kyushu University email:marcin+*+cube.kyushu-u.ac.jp From owner-chemistry@ccl.net Sun Dec 11 21:23:00 2005 From: "Paul Tratnyek tratnyek---ebs.ogi.edu" To: CCL Subject: CCL: Wiki-like Chemical Databases Message-Id: <-30278-051211200304-4110-gG2tyRiavE0YdQF3M/CbWw(!)server.ccl.net> X-Original-From: Paul Tratnyek Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Sun, 11 Dec 2005 16:25:20 -0800 Mime-Version: 1.0 Sent to CCL by: Paul Tratnyek [tratnyek__ebs.ogi.edu] Any examples of--or software for--implementing "open" databases of physicochemical data were anyone can contribute to the database via the web, as in the wikipedia and other wiki-based databases of other kinds of information. Thanks. From owner-chemistry@ccl.net Sun Dec 11 23:39:00 2005 From: "Ricardo Mancera r.mancera .. wabri.org.au" To: CCL Subject: CCL: Molecular Modelling 2006 (MM2006) - Last Call for Abstracts Message-Id: <-30279-051211233533-21238-7jb4iJb3bU5U1Mj7msU9vw=-=server.ccl.net> X-Original-From: "Ricardo Mancera" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 12 Dec 2005 12:34:30 +0800 MIME-Version: 1.0 Sent to CCL by: "Ricardo Mancera" [r.mancera#%#wabri.org.au] MOLECULAR MODELLING 2006 (MM2006) - PERTH, AUSTRALIA, 19-22 APRIL 2006 *** LAST CALL FOR ABSTRACTS *** DEADLINE FOR ABSTRACT SUBMISSION: *** Friday 16 December 2005 *** DEADLINE FOR STUDENT BURSARY APPLICATION: *** Friday 16 December 2005 *** We are pleased to announce that Molecular Modelling 2006 (MM2006) will be held in Perth, Australia from Wednesday 19 until Saturday 22 of April 2006 at Curtin University of Technology. These series of meetings are held every 18-24 months and aim to bring together the modelling community in Australia, New Zealand, the Asia-Pacific region and other parts of the world. The members of the organising committee are Ricardo Mancera (chair), Julian Gale, Andrew Rohl, Mark Spackman and Sue Berners-Price. The Conference Secretary is Kate Wright. CALL FOR ABSTRACTS MM2006 will cover molecular modelling in the life and physical sciences. Abstracts are invited for both oral and poster contributions in the broad areas of biomolecular modelling (protein and macromolecular modelling, ligand- and structure-based drug design and general molecular modelling), computational chemistry (ab initio, DFT and QM/MM methods) and materials modelling (condensed matter and polymers). Abstracts should be no longer than one page long and submitted by e-mail as Word or RTF documents to the Conference Secretariat. Abstracts should include a title, names of authors and their affiliations, summary of the work presented and references. Figures may be included within the one-page limit, but reproduction will be done in black and white only. PROCEEDINGS The proceedings of the meeting will be published in a special issue of the journal Molecular Simulation. Participants of the meeting will be invited to submit papers, which will undergo peer review. LIST OF CONFIRMED SPEAKERS In keeping with previous conference formats, we will have a number of plenary speakers (mostly from overseas) as well as invited and contributed presentations. We will also hold a poster session. This is the list of confirmed speakers so far: Prof Alan Mark (University of Queensland Dr Mark Smythe (University of Queensland Prof Jill Gready (Australian National University Dr Renate Griffith (University of Newcastle) Dr David Chalmers (Monash University) Dr Brian Smith (Walter and Eliza Hall Institute of Medical Research) Dr Bret Church (University of New South Wales) Dr Merridee Wouters (Victor Chang Cardiac Research Institute) Prof Peter Gill (Australian National University) Prof Sean Smith (University of Queensland) A/Prof Billy Todd (Swinburne University) Prof Ian Snook (RMIT) Dr Oliver Warschkow (University of Sydney) Dr Chandra Verma (Bioinformatics Institute, Singapore) Prof Kyoung Tai No (Yonsei University, Korea) Dr Jed Pitera (IBM Almaden Research Centre, USA) Prof Brian Shoichet (University of California, San Francisco, USA) Dr Jonathan Essex (University of Southampton, UK) Prof Alessandro Laio (ETH Zurich, Switzerland) Prof Simon Phillpot (University of Florida, USA) STUDENT BURSARIES We will be offering a number of student bursaries that will cover the registration fee and provide partial reimbursemente of travel expenses. Between 2 and 3 of these bursaries will be sponsored by Accelrys for work that is being carried out using any of their suites of molecular modelling softwares. REGISTRATION The organising committee would like to invite you to register for this meeting. The conference website has all appropriate forms for registration and application for student bursaries, as well as information about abstract submission. Please point your browsers to: http://www.nanochemistry.curtin.edu.au/conferences/mm_2006.cfm KEY DATES Abstract submission deadline: Friday 16 December 2005 Student bursary application deadline: Friday 16 December 2005 Earlybird registration deadline: Friday 18 February 2006 We would be delighted if you can join us next year here in Perth. Please circulate this announcement to others who might be interested in attending. We look forward to welcoming you to Perth next year! Ricardo Mancera (on behalf of the Organising Committee) ------------------------------------------------------------------------ ---------- Ricardo L. Mancera, M.A., Ph.D. Senior Research Fellow Western Australian Biomedical Research Institute & School of Pharmacy and School of Biomedical Sciences Curtin University of Technology GPO Box U1987 Perth WA 6845 Australia Tel: +61 8 9266 1017 Fax: +61 8 9266 7485 E-mail: R.Mancera a wabri.org.au R.Mancera a curtin.edu.au