From chemistry-request@ccl.net Thu May 29 16:32:07 2003 Received: from web10405.mail.yahoo.com (web10405.mail.yahoo.com [216.136.130.97]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h4TKW7gC017967 for ; Thu, 29 May 2003 16:32:07 -0400 Message-ID: <20030529203207.16158.qmail{at}web10405.mail.yahoo.com> Received: from [40.0.40.10] by web10405.mail.yahoo.com via HTTP; Thu, 29 May 2003 13:32:07 PDT Date: Thu, 29 May 2003 13:32:07 -0700 (PDT) From: Guosheng Wu Subject: CCL: Orbitals To: Sengen Sun Cc: chemistry{at}ccl.net In-Reply-To: <20030529172126.5031.qmail{at}web20609.mail.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii A few words about Orbitals and QM. If Einstein was one of those who first discovered Quantum Mechanics, he might have had different opinion about it, which partly would make it easy for many others to accept it earlier than later. It is just because QM is so great and he was also so great... There seems no conceptual or logical conflicts about QM. It's just about wave_like_properties described with MO(Molecular Orbital) or WF(wavefunction), no matter how sophisticated it may be, and properties from it(propability, energies...) by something like . Put time into the operator and elsewhere properly if one is interested in the properties of dynamics. By the way, it seems to me MO is mostly seen as just an essentially same concept as WF. "MO" is still used at least in this list, just like any piece of a language, or the formation of a physical road ... As a mathematical problem for a MODEL system, it had certainly been solved accurately by QM, in the scope of atoms & electrons in the vacum. For the real world problems, most people and many in this list are just playing with Applied Maths & computers to get something useful in some areas of chemistry, materials or biology. That's it, like Direc ever said. Guosheng --- Sengen Sun wrote: > E. Lewars wrote: > > If MOs have no physical reality for multielectron > species, why (a) is Koopmans' theorem useful, why (b) > do photoelectron spectra match the predictions of MO > energy-level diagrams, and why (c) does the Hueckel > 4n+2 rule, which is based on MO diagrams, work? > > These are extremely interesting questions to me. They > are very difficult to be answered, as implied by two > very prominent theoretical physicists in the last > century Gell-Mann and Feynman: > http://www.prometheus.demon.co.uk/02/02kumar.htm > > I agree with Scerri, Spanget-Larsen, and many others > that MOs have no physical reality. But I don t think > that we, as suggested by Feynman, should stop asking > why MOs are so powerful for predictions in chemistry. > If we stop thinking, we would accept the control of > the universe by something of no physical reality; And > we would not be able to achieve a real understanding > of chemistry and the universe; And we would have > conceptual or logical conflicts... > > > __________________________________ > Do you Yahoo!? > Yahoo! Calendar - Free online calendar with sync to Outlook(TM). > http://calendar.yahoo.com > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY{at}ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl{at}ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com From chemistry-request@ccl.net Thu May 29 16:38:51 2003 Received: from facepe.dqf.ufpe.br (facepe.dqf.ufpe.br [150.161.5.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4TKcngC018218 for ; Thu, 29 May 2003 16:38:51 -0400 Received: from dqf.ufpe.br ([150.161.5.90]) by facepe.dqf.ufpe.br (8.12.6/8.12.6) with ESMTP id h4TI9hfD019199; Thu, 29 May 2003 15:09:43 -0300 (BRT) (envelope-from sidney$at$dqf.ufpe.br) Message-ID: <3ED6732B.2070001$at$dqf.ufpe.br> Date: Thu, 29 May 2003 17:52:59 -0300 From: Sidney Ramos de Santana User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL List Subject: Dalton 1.2 Problem: wave function not converged! Content-Type: multipart/mixed; boundary="------------080901090907070203060208" This is a multi-part message in MIME format. --------------080901090907070203060208 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCL Users, I have been trying to perform a Shieldings and Spin-Spin Couplins Constants calculations with Dalton 1.2 for Pt[(SnCl3)4]3-. I am using ECP but I don't have sucessful. Please see below: Basis Set Section: ------------------------ label atoms charge prim cont basis ---------------------------------------------------------------------- Pt 1 18 46 32 [9s5p3d1f|3s4p2d1f] ... Sn 1 4 17 13 [3s3p1d|2s2p1d] ... Cl 1 7 17 13 [3s3p1d|2s2p1d] ---------------------------------------------------------------------- total: 21 143 386 292 ---------------------------------------------------------------------- Sirius Section: ------------------- *** Optimization control WARNING: MCSCF not converged *** Maximum number of iterations or backsteps reached: Number of macro iterations used 5 Maximum 15 Number of micro iterations used 47 Maximum 180 Number of back steps this macro 6 Maximum 5 Total number of CPU seconds used 195396.71 WARNING: wave function not converged End of File: ---------------- - DALTON aborted because wave function not converged! --- SEVERE ERROR, PROGRAM WILL BE ABORTED --- Date and time (SUN) : Mon May 26 22:47:46 2003 Host name : samba Reason: DALTON aborted because wave function not converged >>>> Total CPU time used in DALTON: 74 hours 48 minutes 59 seconds >>>> Total wall time used in DALTON: 77 hours 50 minutes 53 seconds Anybody Can Help me ? What can I do ? Sidney Ramos Graduate Program of Materials Science CCEN - DQF - UFPE - Brazil --------------080901090907070203060208 Content-Type: text/plain; name="complex1.dal" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="complex1.dal" **DALTON INPUT .RUN PROPERTIES .DIRECT **WAVE FUNCTION .HF **PROPERTIES .SHIELD .SPIN-S *SPIN-S .ABUNDA 0.10 .SELECT 5 1 3 4 5 6 *END OF INPUT --------------080901090907070203060208 Content-Type: text/plain; name="complex1.mol" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="complex1.mol" BASIS ECP NMR parameters - Geom. Optimized 12345678901234567890123456789012345678901234567890 3 -3 78. 1 Pt -0.000033 -0.000283 -0.000186 50. 5 Sn -0.000080 -1.570825 -2.048043 Sn -0.000039 -0.990691 2.382968 Sn 0.000162 2.558780 -0.334569 Sn 2.554395 0.001166 -0.000422 Sn -2.554461 0.001405 -0.000410 17. 15 Cl -3.802978 -1.942611 0.750175 Cl -3.799062 0.326369 -2.061309 Cl -3.798572 1.625239 1.309935 Cl 3.802841 -1.942389 0.751459 Cl 3.798619 1.625839 1.308775 Cl 3.798953 0.324672 -2.061577 Cl 0.001018 -3.426703 2.638517 Cl -1.772298 -0.579453 4.015542 Cl 1.771227 -0.577884 4.016225 Cl -1.772125 -3.191337 -2.504964 Cl 1.770880 -3.192816 -2.503934 Cl 0.000995 -0.577499 -4.286911 Cl 0.001882 3.998926 1.646483 Cl -1.772925 3.765926 -1.506748 Cl 1.771766 3.765506 -1.509414 --------------080901090907070203060208-- From chemistry-request@ccl.net Thu May 29 17:29:55 2003 Received: from facepe.dqf.ufpe.br (facepe.dqf.ufpe.br [150.161.5.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4TLTsgC019003 for ; Thu, 29 May 2003 17:29:55 -0400 Received: from dqf.ufpe.br ([150.161.5.90]) by facepe.dqf.ufpe.br (8.12.6/8.12.6) with ESMTP id h4TJ0wfD019275 for ; Thu, 29 May 2003 16:00:58 -0300 (BRT) (envelope-from sidney$at$dqf.ufpe.br) Message-ID: <3ED67F2E.9090506$at$dqf.ufpe.br> Date: Thu, 29 May 2003 18:44:14 -0300 From: Sidney Ramos de Santana User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL List Subject: Random Number Generator Fail ... Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCL Users, I compiled the Shell-Dynamo 2.1 with G77(Gnu Compiler) and with IFC(Intel Fortran Compiler). I have been trying to perform a calculation of diffusion constants of Ions in a oxifluoride glass. In this program I am using Buckigham potential and the initial coordinates of the ions in the simulation box was been filling randomicly, because I choosed the option "fillbox random". This initial coordinates in the program compiled with G77 are generating by "ranf" intrinsic function, and in the IFC are generating by "random_number" intrinsic function using "date_and_time" intrinsic function to generate a seed. In the both cases the initial configuration generated was the worst possible. This way, I will need a very, very big step numbers in this MD simulation. So, this question for you: What is the best to generate randomicly an initial coordinates of the ions the simulation box: an intrinsic function of Compiler to generate random number (if yes, why?) or an algorithm(if yes, why) ? Sidney Ramos Graduate Program of Materials Science DQF - CCEN - UFPE From chemistry-request@ccl.net Fri May 30 02:29:17 2003 Received: from maties3.sun.ac.za (maties3.sun.ac.za [146.232.128.43]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4U6TGgC029979 for ; Fri, 30 May 2003 02:29:16 -0400 Received: from stbex02.stb.sun.ac.za ([146.232.20.17] helo=STBEVS01.stb.sun.ac.za) by maties3.sun.ac.za with esmtp (Exim 4.10) id 19LdO6-0007FO-01; Fri, 30 May 2003 08:29:14 +0200 X-MimeOLE: Produced By Microsoft Exchange V6.0.6334.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: CCL:RE: Eigenvalues of hessian Date: Fri, 30 May 2003 08:28:41 +0200 Message-ID: <21F5207AECE530428EBD1EBF78DA95B77944AF:at:STBEVS01.stb.sun.ac.za> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Eigenvalues of hessian Thread-Index: AcMl4vF2keZPpRh9SAORK/6cVHS57gAi8erw From: "Dillen Jan " To: Cc: "Daniel R. Rohr" X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *19LdO6-0007FO-01*7JMWuRSrVQc* Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h4U6THgC029980 > I do know that in the Hessians calculated, there is usually > translation > and rotation. I want to avoid speaking of frequencies, because we are > talking about Hessians which are not necessarily calculated at > stationary points. Dear Daniel, The fact that frequencies are equal to the square root of the diagonalised mass-weighted Hessian matrix is a result obtained from solving the following equations of motions: F = m.a = - H.dx where 'm' is a diagonal mass matrix, 'a' the acceleration, 'H' the Hessian, and 'dx' are the displacement coordinates. The 'H.dx' appears if one assumes that (1) the potential energy can be written as a harmonic function of the displacement coordinates and (2) that the gradient vanishes, i.e. U = U(0) + 1/2 (dx)^T.H.dx (1) is called the harmonic approximation and (2) implies a stationary point. Hence "frequencies" which are not calculated at a stationary point do not necessarily have zero translational and rotational components. Here is an alternative reasoning. The potential energy should not change if the molecule is translated, i.e. dU/dX = 0 with 'X' are the coordinates of the centre of mass. However, dU/dX = sum (dU/dx) (dx/dX) where 'x' are atomic coordinates. More complex expressions appear for the second derivatives. Obviously, dX/dx is not zero (and hence also dx/dX), so dU/dx must be zero in order to have dU/dX = 0, i.e. a stationary point. (or if the sum of these terms happens to be exactly zero) Hope this helps. Groeten Jan Dillen From chemistry-request@ccl.net Fri May 30 08:07:56 2003 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4UC7tgC008354 for ; Fri, 30 May 2003 08:07:55 -0400 Received: (from assfeld@localhost) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) id OAA26570 for chemistry-.at.-ccl.net; Fri, 30 May 2003 14:06:18 +0200 Date: Fri, 30 May 2003 14:06:18 +0200 From: assfeld-.at.-host20.lctn.uhp-nancy.fr Message-Id: <200305301206.OAA26570-.at.-host20.lctn.uhp-nancy.fr> To: chemistry-.at.-ccl.net Subject: CCL: Orbitals Hey, Just to throw oil on fire.... Of course orbitals (molecular, atomic...) are not "real", because they just result from the mathematical construction of our theory. They are not unique, and so on... But is the many electrons wave function (Y) more "real"? Parentheses: Ok, I know that wave function are not real, only the square (YY*) has a physical meaning. But I prefer to speak about wave function, knowing that the observable density is deduced from this wave function. End Parentheses. What I mean is that: - The exact Hamiltonien (fully relativistic, not B-O,...) is generally not used (not known?). Then the exact solutions we have are just solution of an approximate Hamiltonien, and thus can not describe exactly the physical phenomenon. - The exact solutions of the (even approximate) Hamiltonien are not known. What we get, is just a more or less acceptable representation of "reality". Does that mean that everything we get with Hartree-Fock method is garbage? The answer is no, because a lot of the "physic" of the system is included in the theory, but it could be improved... Does someone remember (or know) why we use orbitals in the first time? I think that it is because they can be exact solutions of approximate Hamiltonien! If, in a model representation of the world surrounding us, we consider that all electrons of a system can move more or less independently from one another, then orbitals are "real" in the sense that they allow us to describe the world with a given level of accuracy. Of course it is not perfect. I really do think that canonical orbitals are "real" because they come > from a theory that has the major physical factor in it (symmetry, nuclear attraction, kinetic energy, average coulombic interaction...). Thus, if one improve the one-electron Hamiltonien (for example with Kohn-Sham method) that gives the canonical orbitals, then orbitals will be more "real" in the sense that they will predict or explain more accurately the world... Well, that was just my 2 eurocents. PS: In reply to E. Lewars, I will even say that virtual orbitals are "real" because they allow us to explain spectroscopy (n -> Pi* transition in H2CO for example) ...Xav Pr. Xavier Assfeld Xavier.Assfeld-.at.-lctn.uhp-nancy.fr Laboratoire de Chimie thiorique (T) 33 3 83 68 43 74 Universiti Henri Poincari (F) 33 3 83 68 43 71 F-54506 Nancy B.P. 239 http://www.lctn.uhp-nancy.fr From chemistry-request@ccl.net Fri May 30 00:40:42 2003 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 h4U4eggC028114 for ; Fri, 30 May 2003 00:40:42 -0400 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by smtp1.server.rpi.edu (8.12.9/8.12.9) with ESMTP id h4U4eeCR016134; Fri, 30 May 2003 00:40:40 -0400 Message-Id: <200305300440.h4U4eeCR016134-.at.-smtp1.server.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: lou-.at.-scripps.edu From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: chemistry-.at.-ccl.net, tlovell-.at.-scripps.edu, wengehan-.at.-scripps.edu, ithink-.at.-san.rr.com, sharples-.at.-scripps.edu, himo-.at.-TheoChem.kth.se X-Originating-Ip: 128.113.135.209 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Fri, 30 May 2003 0:40:40 EDT X-Mailer: EMUmail 4.00 Subject: Re: CCL:Orbitals and Reality X-Scanned-By: MIMEDefang 2.28 Dr. Noodleman, I hate to quibble with what you've written, since you've expressed things so clearly, and I agree with most of what you say, but... > In general, I think of orbitals as somewhat real, less than electron > densities, or atoms, > but more than Lewis bond structures (at least, most of the time). I think of orbitals as somewhat LESS real than "Lewis bond structures" since in most cases the latter can be uniquely derived from topological analysis of the (real) electron-density, i.e. from the gradient paths and critical points thereof, whereas individual one-electron orbitals for many-electron systems, however useful they might be, are quite arbitrary; orbitals are solutions to a mathematical equation for a model system and will differ depending upon the model employed (Huckel, Hartree-Fock, Kohn-Sham, natural orbitals). With all due respect to the stalwarts of quantum mechanics, it makes little sense today to use terms like "physical reality" which cannot be defined with the degree of rigor we expect in science, without employing circular logic. And how to define "think" and "I" without invoking open systems and wavefunction collapse? Why, I'll be glad if we can all agree on the meaning of the word "is"! Dr. N. Sukumar http://www.drugmining.com/ Visiting Scientist Rensselaer Department of Chemistry and Wadsworth Center, New York State Dept.of Health From chemistry-request@ccl.net Fri May 30 01:02:18 2003 Received: from puck.reed.edu (puck.reed.edu [134.10.2.8]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h4U52IgC028493 for ; Fri, 30 May 2003 01:02:18 -0400 Received: (qmail 27369 invoked from network); 30 May 2003 05:02:18 -0000 Received: from rosencrantz.reed.edu (134.10.2.31) by puck.reed.edu with SMTP; 30 May 2003 05:02:18 -0000 Message-id: <14170429-.at.-rosencrantz.reed.edu> Date: 29 May 2003 22:02:13 PDT From: Alan.Shusterman-.at.-directory.reed.edu (Alan Shusterman) Subject: CCL: Orbitals and Reality To: chemistry-.at.-ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h4U52IgC028496 This discussion has taken some very unexpected and interesting twists. I want to put in my 2 cents regarding two interesting ideas that have appeared today... 1. Orbitals may only be mathematical constructs, but since they explain so much (scattering expts, PES, Woodward-Hoffman rules, aromaticity, etc.), they *feel* real and ought to be accepted as such 2. All of our theories contain approximations, so we are not justified in calling anything "real" that we calculate Response to 1. I think this proposal has emotional appeal, and therein lies the problem. Take Woodward-Hoffman rules. They are just one of the many ways to explain what goes on in a pericyclic transition state. Or, take aromaticity. The traditional pi MO explanation of aromaticity was successfully challenged over a decade ago. Finally, take PES spectra - one can find PES spectra that fit MO energy sequences nicely and others that don't. Knowing the limitations of, and alternatives to, MO-based rationales does not make MOs less useful, but it should temper one's emotional attachment to them. The fact that MOs display interesting properties does not make them real. Conversely, the fact that they are only mathematical constructs does not prevent them from being interesting or useful. Response to 2. Lou Noodleman points out the many layers of approximation embedded in ab initio computations. I think his argument may be a red herring, however. When we calculate energy, we calculate an *estimate* (subject to one or more of the approximations Lou listed) of an observable quantity. It's true that if we remove an approximation (Born-Oppenheimer, lack of relativistic effects, etc.) we must change the methodology used to estimate the molecular energy, but we continue to estimate *molecular energy*. Furthermore, we can compare our estimate to experiment, and learn about the significance of these approximations. The situation is different for wavefunctions and MOs. First, these are mathematical constructs that can't be compared to any observable quantities except by introducing a theory or rationale that says "wavefunction/MO property Z should correlate with observable X". Second, and more important for this discussion, MOs only appear when we assume independent electron behavior (which is the most extreme approximation that we can make). This seems to make MOs rather special - you can write wavefunctions that cannot be factored into MOs. They do not simply adjust their values, like the molecular energy does, as approximations are added or removed. (I hope this won't look like hair-splitting when I read this tomorrow morning) -Alan ==== Alan Shusterman Department of Chemistry Reed College 3203 S.E. Woodstock Blvd. Portland, OR 97202-8199 503-517-7699 From chemistry-request@ccl.net Fri May 30 05:08:32 2003 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4U98VgC001935 for ; Fri, 30 May 2003 05:08:31 -0400 Received: from pop-c.ucl.ac.uk by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 30 May 2003 10:08:29 +0100 Received: from pop-d.ucl.ac.uk (pop-d.ucl.ac.uk [144.82.100.34]) by pop-c.ucl.ac.uk (8.11.7+Sun/8.10.2) with ESMTP id h4U98OE22167 for ; Fri, 30 May 2003 10:08:24 +0100 (BST) Sender: mb.-at-.ucl.ac.uk Message-ID: <3ED71BD4.3B63B7F1.-at-.ucl.ac.uk> Date: Fri, 30 May 2003 09:52:36 +0100 From: M Brunsteiner Organization: UCL X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry.-at-.ccl.net Subject: docking software for molecule-surface affinity ? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCL-MailScanner: Found to be clean Dear all, Can anybody point me to a (preferably free are reasonably priced) software that can do docking between a given surface structure and a range of organic molecules/polymers ? Can any of the programs that are used for bio-receptor/ligand or protein-protein interactions (such as dock, autodock flexx, etc) be used for this purpose ? thanks in advance for any help! cheers, Michael ========================================================================== "Emotions are alien to me. I'm a scientist." (Spock, "This Side of Paradise", stardate 3417.3) -------------------------------------------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London mailto:m.brunsteiner.-at-.ucl.ac.uk http://www.ucl.ac.uk/~uccambr/ -------------------------------------------------------------------------- From chemistry-request@ccl.net Fri May 30 03:51:42 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4U7pfgC032527 for ; Fri, 30 May 2003 03:51:42 -0400 Received: from moka.ccr.jussieu.fr (moka.ccr.jussieu.fr [134.157.1.23]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h4U7peru003156 for ; Fri, 30 May 2003 09:51:40 +0200 (CEST) Received: from ccr.jussieu.fr (IDENT:jeo.-at-.mozart.div.jussieu.fr [134.157.75.159]) by moka.ccr.jussieu.fr (8.10.0/jtpda-5.3.3) with ESMTP id h4U7peE807060 for ; Fri, 30 May 2003 09:51:40 +0200 Message-ID: <3ED7045B.6090004.-at-.ccr.jussieu.fr> Date: Fri, 30 May 2003 09:12:27 +0200 From: Sebastien Laugaro User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY.-at-.ccl.net Subject: Gaussian problem Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Antivirus: scanned by sophie at shiva.jussieu.fr Hy, I work on Gaussian and I have a problem. In fact, when I use B3LYP/6-31G* OPT TEST Int(Grid=35110) , I have a error message : 'Convergence Failure. Error Termination'. When I use the same file and HF/STO-3G OPT TEST Int(Grid=35110), I have no problem. Can you help me to resolve my problem. Thank you. Sebastien. laugaro.-at-.ccr.jussieu.fr From chemistry-request@ccl.net Fri May 30 10:50:37 2003 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4UEoagC015947 for ; Fri, 30 May 2003 10:50:37 -0400 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.1-1 #30546) id <01KWICZWFMOG000S76^at^cuces.unisi.it> for chemistry^at^ccl.net; Fri, 30 May 2003 16:50:30 +0100 (MET) Received: from unisi.it (ccmaol10.chim.unisi.it [172.16.29.96]) by cuces.unisi.it (PMDF V6.1-1 #30546) with ESMTPA id <01KWICZVP9QS000WYZ^at^cuces.unisi.it> for chemistry^at^ccl.net; Fri, 30 May 2003 16:50:30 +0100 (MET) Date: Fri, 30 May 2003 16:41:48 +0200 From: "Nicolas Ferre'" Subject: CCL: QM/MM cutoffs Sender: ferre^at^unisi.it To: chemistry^at^ccl.net Message-id: <3ED76DAC.EB291CEB^at^unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.78iC-CCK-MCD [en_US] (X11; U; AIX 5.1) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi folks, I'm currently implementing a simple QM/MM molecular dynamics approach, but I have some doubts about the right way of dealing with the electrostatic interactions between the quantum distribution and the classical point charges. Using periodic boundary conditions and the minimum image convention, I have to define a cutoff distance : a site-site interaction is discarded if the site-site distance is greater than this value. OK for a classical simulation. Now if part of the system is treated quantum mechanically, the definition of some QM sites is non-obvious : the QM wavefunction is delocalized on the whole QM subsystem. The simplest idea would be to select the center of mass of the QM subsystem as a unique site only to choose MM point charges interacting with the QM subsystem, but if the QM molecular shape is not spherical, this solution is not convenient (a QM atom located at one end of the QM subsystem could not interact with the closest images of some MM point charges). Thus I'd like to hear about your solutions/experiences/references to solve this problem, taking in mind that I don't want to approximate (for the moment) the QM electronic distribution (no fitted multipoles ...) I know about Ewald sums for QM/MM interactions but I'd prefer to start with a rather simplest approach. Best regards, Nicolas -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre^at^unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@ccl.net Fri May 30 11:39:49 2003 Received: from sungoddess.ccs.yorku.ca (sungoddess.ccs.yorku.ca [130.63.236.144]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4UFdngC017546 for ; Fri, 30 May 2003 11:39:49 -0400 Received: from mountain.chem.yorku.ca (mountain.chem.yorku.ca [130.63.133.28]) by sungoddess.ccs.yorku.ca (8.12.9/8.12.8) with SMTP id h4UFdj0P010372 for ; Fri, 30 May 2003 11:39:45 -0400 (EDT) Date: Fri, 30 May 2003 11:27:21 -0400 (EDT) From: Rene Fournier - 1999-07-07 X-Sender: renef)at(mountain.chem.yorku.ca To: chemistry)at(ccl.net Subject: Orbitals In-Reply-To: <200305301206.OAA26570)at(host20.lctn.uhp-nancy.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I agree with Lou Noodleman's point that we have many mathematical models with different degrees of rigor to approach reality without ever quite reaching it (sounds like calculus...). And I do like orbitals, especially Kohn-Sham orbitals, a lot. But I think there's a difference between, say, an approximate electron density -- far from reality because it is inaccurate -- and a set of orbitals -- far from reality because we're not sure exactly what kind of measurements they should be compared to. That being said, theoretical arguments and comparisons to experiments support the view that KS orbital energies are good approximations to relaxed vertical ionization potentials (Chong, Gritsenko, Baerends, J Chem Phys 116 (2002) 1760), that differences of virtual and occupied KS orbital energies are good approximations to excitation energies (A Savin, CJ Umrigar, X Gonze, Chem Phys Lett 288 (1998) 391), that KS orbitals give good approximations to spherically averaged momentum distributions obtained by electron momentum spectroscopy (P Duffy, DP Chong, ME Casida, DR Salahub, Phys Rev A 50 (1994) 4707; S Hamel, P Duffy, ME Casida, DR Salahub Journal of Electron Spectroscopy and Related Phenomena (2002?)). To me, KS orbitals are meaningful, and are useful for quantitative comparisons even though it's not 100% clear what they should be compared with. Whether they are "real" in some particular philosophical system is not as important for me... but it's still interesting! :) -- Rene Fournier. -------------------------------------------------------------------- | Rene Fournier | Office: 303 Petrie | | Chemistry Dpt, York University| Phone: (416) 736 2100 Ext. 30687 | | 4700 Keele Street, Toronto | FAX: (416)-736-5936 | | Ontario, CANADA M3J 1P3 | e-mail: renef)at(yorku.ca | -------------------------------------------------------------------- From chemistry-request@ccl.net Fri May 30 19:00:38 2003 Received: from einstein.physics.drexel.edu (einstein.physics.drexel.edu [129.25.7.60]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4UN0bgC000537 for ; Fri, 30 May 2003 19:00:38 -0400 Received: from silicon.physics.drexel.edu (silicon.physics.drexel.edu [129.25.8.33]) by einstein.physics.drexel.edu (8.11.6/8.11.6) with ESMTP id h4UN4wF03981 for ; Fri, 30 May 2003 19:04:58 -0400 Date: Fri, 30 May 2003 19:00:43 -0400 (EDT) From: Avijit Ghosh To: chemistry/at/ccl.net Subject: Re: CCL:Orbitals In-Reply-To: <5CF08BBFE6DE97478C1E76E654CAF90801BC0BEC/at/lvlxch02.ntdomain.americas.sc-world.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, let me first qualify this as I am far removed from quantum dynamics/electronic structure/semiclassical physics and am just putting some thoughts in as someone who has been listening to the discussion w/ great interest. I think orbitals used as "basis set expansions" as in many electronic structure calculations might be considered a mathematical trick to solve a differential equation and there should be treated as mathematical constructs since they are being treated as such. However there are several issues here. (1) If I take the term orbital to mean the "wave function" of a single e-, is it "real"? I would say no as the wave function is a thing that exists in complex space and is not as such observable property. In this sense the "many e-" wavefunction is not observable either, so that statement I think has less to do w/ "orbitals" but more to do w/ wavefunctions as the thing that one "operates" on to get observables. (2) Does the single e- wavefunction density have any meaning? Let me decompose this a bit. To me the fact that organic chemists can "hybridize" orbitals (aka "handwaving quantum mechanics") is a testament to the contribution of e-e- correlation as actually not being that much at least for the first part of the periodic table. In fact that elements have the properties that they do is also a testament to this. Let me rephrase this w/ a model, suppose epsilon_0 for e-e- interactions only were some other value. That is we could scale down the correlation function, at arbitrarily small scaling (i.e large epsilon_0) the "orbital" approximation (as observable single e- densities) By construction the "orbital" approximation is closer to "reality" as I scale my hamiltonian. That is the wavefunction would become a product of single e- wavefunctions, even though technically I can not *ever* write the wavefunction as a product of single e- wavefunctions as long as I have even an arbitrarily small amount of e-e- correlation. I think that the assertion of orbitals "existing" is just an assertion of that e-e- is 0.5 % of the answer allowing the organic chemists to "write" the wavefunction as a product of single e- wavefunctions. It seems to me that if one is allowed to posit the total electronic wavefunction density has a "reality" on its own and corresponding measurements and eigenstates (i.e. decoupling the nuclear/electronic kinetic terms ala born oppenheimer) as having a reality, then one in the same manner should be allowed to posit orbitals as having a "reality" since it seems to me to be the same approximation just on a different part of the hamiltonian. -avi Asst. Prof. Avijit Ghosh Dept of Physics Drexel University From chemistry-request@ccl.net Fri May 30 14:23:54 2003 Received: from hotmail.com (law10-oe19.law10.hotmail.com [64.4.14.123]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4UINrgC024297 for ; Fri, 30 May 2003 14:23:54 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 30 May 2003 11:23:53 -0700 Received: from 146.244.232.26 by oe19.law10.hotmail.com with DAV; Fri, 30 May 2003 18:23:52 +0000 X-Originating-IP: [146.244.232.26] X-Originating-Email: [czeinalip_at_hotmail.com] From: "Zeinalipour-Yazdi Constantinos" To: "Computational Chemistry list" Subject: CCL: STM simulation package Date: Sat, 31 May 2003 11:14:13 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0063_01C32765.C41BC400" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Message-ID: X-OriginalArrivalTime: 30 May 2003 18:23:53.0166 (UTC) FILETIME=[9FC316E0:01C326D8] This is a multi-part message in MIME format. ------=_NextPart_000_0063_01C32765.C41BC400 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLer's, I am trying to find a software that can simulate the STM image of a DFT = calculation using HF/B3LYP. I am currently using GAMESS/US as my = computational tool.=20 Best regards, Constantinos. Zeinalipour-Yazdi Constantinos PhD student Department of Chemistry San Diego State University University of California, San Diego Lab phone : (619)-594-2002 ------=_NextPart_000_0063_01C32765.C41BC400 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLer's,
 
I am trying to find a software = that can=20 simulate the STM image of a DFT calculation using HF/B3LYP. I am = currently using=20 GAMESS/US as my computational tool.
 
Best regards, = Constantinos.
 
Zeinalipour-Yazdi Constantinos
PhD=20 student
Department of Chemistry
San Diego State = University
University=20 of California, San Diego

Lab phone :=20 (619)-594-2002
------=_NextPart_000_0063_01C32765.C41BC400-- From chemistry-request@ccl.net Fri May 30 19:07:54 2003 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4UN7rgC000771 for ; Fri, 30 May 2003 19:07:53 -0400 Received: from [128.97.147.207] (ch-07.psnet.ucla.edu [128.97.147.207]) (authenticated bits=0) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id h4UN7l7s012806 for ; Fri, 30 May 2003 16:07:52 -0700 Mime-Version: 1.0 X-Sender: scerri_at_chlorine.chem.ucla.edu (Unverified) Message-Id: Date: Fri, 30 May 2003 16:07:46 -0700 To: ccl From: Eric Scerri Subject: orbitals Content-Type: text/plain; charset="us-ascii" ; format="flowed" As somebody working in philosophy of science and more specifically philosophy of chemistry I have found the recent discussion very interesting. Although I may not have fully digested every subtle nuance and technicality concerning orbitals that has been voiced in recent days I believe I may still be able to contribute to one major aspect of the discussion. This is on the question of usefulness and reality. There is a long-standing debate in philosophy of science going back for hundreds of years which in modern terminology is referred to as the realism versus anti-realism debate. Very briefly realists believe that we can attribute physical reality to scientific terms that are used in successful scientific theories regardless of whether or not these terms can be observed. Indeed most realists believe that we should attribute physical reality to unobservable terms or entities like quarks. Modern realism arose as a reaction against logical positivism whereby every scientific term would need to be grounded in observation. The failure of the program of logical positivism (Carnap, Schlick, Nagel, Reichenbach etc.) came about for many reasons among them being the inability to draw a sharp distinction between theoretical and observational terms. But logical positivism has not died away altogether and there is a sense in which it survives in the modern anti-realism view of scientific theories. According to this view, of which Bas van Fraassen is the leading proponent, observability remains an important criterion. If a scientific term or entity cannot or has not been observed then we have no warrant for assigning physical reality to it. No matter how useful a scientific theory or scientific term might be this does not warrant us in the further belief that this theory or particular scientific term might have physical reality. As I mentioned in an earlier posting there have been many terms that were temporarily useful in now defunct theories. For example phlogiston was initially quite useful and successful in explaining many chemical facts. Some people may even have believed that this meant that phlogiston was a real physical entity and yet as everybody knows it turned out to be a mistake. Of course I am not suggesting that orbitals will necessarily turn out be be a mistake, except in the general sense that all scientific theories and approaches are eventually refuted. This view, called the pessimistic meta-induction, provides a rather powerful argument against regarding any scientific theory realistically and similarly any scientific terms from current theories. Finally, it should also be recalled that the most widely held interpretation of quantum mechanics, the Copenhagen interpretation, is essentially an anti-realistic interpretation regardless of what people like Einstein and David Bohm may have wanted. So it is a little puzzling to discover that some quantum chemists are prepared to go beyond this general philosophical framework when it comes to one particular term within quantum chemistry and to attribute physical reality to orbitals. regards, eric scerri -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri_at_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://www.georgetown.edu/earleyj/ISPC.html