From chemistry-request@ccl.net Thu Feb 24 01:42:51 2005 Received: from smtp1.server.rpi.edu (smtp1.server.rpi.edu [128.113.2.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1O6gn63021526 for ; Thu, 24 Feb 2005 01:42:49 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by smtp1.server.rpi.edu (8.13.0/8.13.0) with ESMTP id j1O6giXc021854; Thu, 24 Feb 2005 01:42:44 -0500 Message-Id: <200502240642.j1O6giXc021854{at}smtp1.server.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: chemistry{at}ccl.net From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: khinsen{at}cea.fr, scerri{at}chem.ucla.edu X-Originating-Ip: 4.141.68.10 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Thu, 24 Feb 2005 1:42:44 EST X-Mailer: EMUmail 4.00 Subject: Re: CCL:orbitals and reality X-CanItPRO-Stream: default X-RPI-SA-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . canit . ca) on 128.113.2.1 X-Spam-Status: No, hits=2.1 required=7.5 tests=COMBINED_FROM,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 On Sat, 19 Feb 2005 15:13:59 -0800 Eric Scerri wrote: > > 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. The reason I, for one, lost interest in this thread was because I do not care to carry on a religious argument for or against orbitals (experiment be damned) with those who believe the rest of the world is deluded. Logical discussion of philosophical points is, however, very much in order. > > 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... > > 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). > > ... > > Now orbitals. > By no stretch of the imagination is there the same mass of evidence > for the physical existence of orbitals! > OK, what about atoms in molecules? Do atoms "exist" within molecules? Do functional groups "exist"? A physicist pre-Bader might have been tempted to answer no. In conventional MO theory or wavefunction based QM, these questions does not make sense. These theories donot make use of these concepts. The concepts are undefined in the theory. But in Bader's theory of atoms in molecules, these questions can definitively be answered in the affirmative. Atoms and functional groups, as virial fragments, are well-defined concepts or objects of the theory. It has been argued here that because the theory of atoms in molecules makes no conceptual use of orbitals, these objects are fictitious or superfluous. Let me clarify that my own research work deals with the theory of atoms in molecules. The flagship program of our group (RECON http://www.drugmining.com) utilizes a database of transferable atom equivalents, defined as virial fragments, for rapid high-throughput descriptor generation, and a similar database of amino acid fragments for proteins (Analytical Chemistry, 73, 5457-5461, 2001; J. Chem. Inf. Comput. Sci. 42, 1347-1357, 2002). Personally I have little conceptual use for orbitals. But orbitals gained the prominence they have today because chemists borrowed these objects from physicists who were concerned with explaining atomic spectra. The fluid dynamical interpretation of quantum mechanics (which has a long and illustrious history all the way back to Madelung and de Broglie) avoids the use of orbitals and deals only with density and phase (or velocity field). But how do we obtain excited state densities of many-electron systems from ground state densities? Orbitals are a useful intermediate concept. Does that bestow an objective reality upon them? For alternative formalisms, see e.g. N. Sukumar and B. M. Deb, Phase Associated with the Single-Particle Density of Many-Electron Systems Intl. J. Quantum Chem. 40, 501-510 (1991). What about molecules themselves? Have molecules been observed? Most chemists would find the question rather silly. However, one can have a perfectly respectable theory of matter without employing the concept of molecules and all experimental observations can be interpreted without positing their existence: Molecules are just resonances in collision theory. To a physicist, a molecule is simply a collision that takes too long. So are molecules "real objects" or just useful (if approximate) concepts? A semantic distinction. On Wed, 23 Feb 2005 20:03:14 +0100 khinsen{at}cea.fr wrote: > > The point I am trying to make is that "reality" has no place in a > scientific theory. The concept belongs to the realm of metaphysics... > -- Exactly the point I too have been making. Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From chemistry-request@ccl.net Thu Feb 24 16:21:10 2005 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1OLL8Y0031762 for ; Thu, 24 Feb 2005 16:21:09 -0500 Received: from caracas-1584.adsl.interware.hu ([213.178.106.48] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.44 #1 (Debian)) id 1D4QPz-0004t3-MO for ; Thu, 24 Feb 2005 22:21:07 +0100 Message-ID: <000f01c51ab7$12fd1380$6401a8c0@cthulhu> From: "Tamas E. Gunda" To: Subject: CCL: Mol2mol upgrade Date: Thu, 24 Feb 2005 22:23:14 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1478 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1478 X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL 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 Members, The new 5.4.0 version of the molecule file conversion, manipulation and utility program Mol2Mol is now available > from http://web.interware.hu/frenzy/mol2mol as trial or shareware version. The current version of Mol2Mol recognizes, and interconverts about 50 different file formats (including subtypes). By entering a format string practically every format can be out/inputted. It can slice multiple structural files to single ones (such as PDB models or MDL SD files to single ones) and vice versa in several variations. Support for PDB Chime subformat (with 1-2-3 bonds). Many molecular utilities. New in Mol2Mol 5.4: - Input of Gaussian output files (now recognized automatically); - Input of Gamess output files (now recognized automatically); (the structures one by one or in browse mode (with charges added)) - Support has been added for the Jmol java applet: MDL mol, XMOL xyz and HyperChem hin files can be written as a javascript variable for using them as inline molecules in html files. - and a few smaller changes, additions In the previous version Mol2Mol 5.3: New utility: - Calculation of Gasteiger-Marsili charges, a simple procedure for calculating partial charges based on electron negativities. Supports organic molecules (C,H,N,O,S,P, halogen atoms). Best suited for systems with unconjugated double bonds only) New geometric utilities: - Calculation and dumping of geometrical data defined by named selections in HyperChem hin or hcs (Hyperchem conformation search) files. - Calculation of the dihedral angle of two best fitted mean planes. In previous versions only the angle of exact planes (defined by three atoms) could by calculated. Now the planes can be defined by any number of atoms. Several small corrections, bug fixes were also made. In the previous version Mol2Mol 5.2: New file format: Hyperchem HCS [conformation search] (read only) New utility: - Superimposing and rms comparison of two molecules; use of all atoms or only selected ones, optionally with different weight factors; it can be done automatically for all structures in multiple files; fitted molecules can be outputted to multiple files. New in POV-Ray format: - bond types are supported in vector mode too; - stereo bond types are supported; - support for rendering elemental symbols in vector mode; - support for rendering atom aliases in 2D sketch files in vector mode; and several bug fixes. Mol2Mol is a very handy set of tools for everybody dealing with molecular modelling. It is impossible to write here all of the features of Mol2Mol, but have a look at its home page: http://web.interware.hu/frenzy/mol2mol POV-Ray fans may also have a look at: http://dragon.unideb.hu/~gundat/povraya.htm The program is available as 30 days unrestricted trial version or as shareware version. Dr. T. E. Gunda