From rull@RUUCI4.chem.ruu.nl Mon May 30 04:42:31 1994 Received: from ruucv1.chem.ruu.nl for rull@RUUCI4.chem.ruu.nl by www.ccl.net (8.6.4/930601.1506) id DAA05509; Mon, 30 May 1994 03:53:13 -0400 Received: from ruuci4.chem.ruu.nl by ruucv1.chem.ruu.nl (5.65b/4.13) with SMTP id AA12388; Mon, 30 May 94 09:53:10 +0200 Received: by RUUCI4 (930416.SGI/930416.SGI.AUTO) for @RUUCV1.chem.ruu.nl:CHEMISTRY@ccl.net id AA05237; Mon, 30 May 94 09:49:49 +0100 From: rull@RUUCI4.chem.ruu.nl (Ton Rullmann) Message-Id: <9405300849.AA05237@RUUCI4> Subject: Re: CCL:phi and psi To: CHEMISTRY@ccl.net Date: Mon, 30 May 1994 09:49:49 +0100 (WDT) Reply-To: rull@ruuci9.chem.ruu.nl In-Reply-To: <9405271404.aa27254@s.s.ms.uky.edu> from "Dr. Leon Y. Xiao" at May 27, 94 10:04:20 am X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 753 Leon Y. Xiao wrote: > Does anybody have a program to calculate the phi and psi angles > for a protein and plot them phi vs. psi? > There is a very good program, called PROCHECK, which calculates and plots many stereochemical properties of proteins, and determines a quality score based on a comparison with structures already in the PDB. The output is in Postscript. For information: gopher://pdb.pdb.bnl.gov/00/Software/Procheck/announce. -- | Ton Rullmann NMR Spectroscopy | | Bijvoet Center for Biomolecular Research | Tel. : int+31.30.533641 | | Utrecht University, Padualaan 8, | Fax : int+31.30.537623 | | 3584 CH Utrecht, The Netherlands | Email: rull@nmr.chem.ruu.nl | From kostd@bgumail.bgu.ac.il Mon May 30 05:42:24 1994 Received: from bgumail.bgu.ac.il for kostd@bgumail.bgu.ac.il by www.ccl.net (8.6.4/930601.1506) id FAA05856; Mon, 30 May 1994 05:17:00 -0400 Received: by bgumail.bgu.ac.il (5.65/DEC-Ultrix/4.3) id AA17077; Mon, 30 May 1994 12:13:56 +0300 Date: Mon, 30 May 1994 11:57:21 +0300 (IDT) From: Daniel Kost Subject: Re: CCL:Light induced torsional movement To: ABRASH@urvax.urich.edu Cc: chemistry@ccl.net In-Reply-To: <01HCWTOA29VM0001WB@urvax.urich.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 29 May 1994 ABRASH@urvax.urich.edu wrote: > Daniel Kost states in a reply to an inquiry by Charles Marais, > " I would just like to comment that a reaction which is induced by > UV light, and the reverse transformation by heat" is quite impossible, since it > would violate the principle of microscopic reversibility: At least in the > thermal part, BOTH the forward and reverse reactions should be "induced" to > the same extent." > > This is completely incorrect. First consider an endothermic reaction with a > delta H = 50 kJ/mol, and an additional activation barrier of 10 kJ/mol. The > energy of activation for the forward reaction will be 60 kJ/mol, and for the > reverse reaction 10 kJ/mol. If the populations of both product and reactant > are initially equal, then at a given temperature, the rate of the reverse > reaction will exceed the rate of the forward reaction, since a larger fraction > of molecules will have the energy necessary to exceed the lower activation > barrier. > > This is an example of a thermal reaction where the forward and reverse > processes are NOT induced to the same extent. The principle of microscopic reversibility states only that the forward and reverse reactions (any thermal reaction) path through the same transition states and intermediates. It says nothing about rates, and the example given above, while by itself correct, is irrelevant. All I meant is that if a reaction is thermally accelerated, i.e. pathes through a lower transition state, the reverse reaction would be equally accelerated in the sense that the same lower transition state would have to be reached. In the above example, the different rates are the consequence of the mass law, i.e. different concentrations, and also the obvious difference in rate constants. Microscopic reversibility would only require that IF the activation barrier for the forward reaction is lowered by, say, 5kJ, the reverse would also be lowered by the same amount. > > But what of microscopic reversibilty? The answer lies in the precise state- > ment of this principle. Laidler in his textbook on chemical kinetics, states > it as follows - "In a system at equilibrium, any molecular process and the > reverse of that process occur on the average at the same rate". The key words > here are AT EQUILIBRIUM. For the type of system above, at equilibrium, the The above, unfortunately, has nothing at all to do with microscopic reversibility. It simply defines the kinetic conditions for equilibrium: equal forward and reverse rates. Microscopic reversibility is not at all restricted to equilibrium conditions. It applies equally to non-equilibrium situations. > probability of a given reactant molecule passing over the activation barrier > to form a product is still much smaller than the probability of a given product > molecule passing over its smaller activation barrier to form products. The > reason that the overall rates of the forward and reverse reactions will > be equal at equilibrium is because in such a system the number of molecules > in the form of reactants will far exceed the number of molecules in the form > of products, and thus the population weighting balances out the energetic > weighting. > > This tells us much about the nature of the system described by our original > correspondent. First, the initial reaction does not lead to an equilibrium > product, but to a system trapped in a state of disequilibrium. Thus the > nascent distribution of products will not be described by microscopic revers- > ibility. Second, this disequilibrium state is populated not thermally, since > [ignore the word since] but by a reaction which occurs on an excited state. > There are several excited state potentials which can result in this type of > disequilibrium. One of the most common has the endothermicity of the > ground state reversed, and has a potential minimum at a nuclear configuration > on the product side of the ground state potential. REaction on such a surface > followed by relaxation to the ground state would result in the type of > photon forward, thermal backward reaction described by our initial > correspondent. > > Sam Abrash > Abrash@URVAX.URICH.EDU > Otherwise, I agree with the writer. Daniel Kost kostd@bgumail.bgu.ac.il From h.rzepa@ic.ac.uk Mon May 30 08:42:26 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id HAA06935; Mon, 30 May 1994 07:52:23 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <01658-0@punch.ic.ac.uk>; Mon, 30 May 1994 12:49:38 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA24681; Mon, 30 May 94 12:49:49 +0100 Message-Id: <9405301149.AA24681@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 May 1994 12:50:02 +0100 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa, Henry) (Rzepa, Henry) Subject: Low cost Stereo viewing glasses Cc: Ben Whitaker , M.Winter@sheffield.ac.uk (Mark_Winter) A company called S3D has recently come to my attention. In about 2 months time, they expect to bring to market LCD shuttered glasses with a wireless IR or cable link, to fit to NTSC or SCSI adaptors, with the purpose of viewing PC and Macintosh monitors operating at <80 Hz in stereo 3D. Whilst the final pricing may change, initial indications are that the IR linked version will be less than $300, and a cable linked version <$100. The product is claimed to use new technology to reduce apparent flicker and to improve performance.S3D do not expect to ship a 120 Hz version immediately, but another company called LAMP may be producing such a version. Of critical importance is whether software will support these glasses. Does anyone know of such developments? At <$100 per system, is this form of 3D viewing likely to take off in chemistry? S3D are on 415 324 8581. I have no afiliation with them. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.02, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From szeinfel@fox.cce.usp.br Mon May 30 09:42:27 1994 Received: from bee08.uspnet.usp.br for szeinfel@fox.cce.usp.br by www.ccl.net (8.6.4/930601.1506) id JAA07295; Mon, 30 May 1994 09:28:42 -0400 Received: from fox.cce.usp.br (fox.cce.usp.br [143.107.70.1]) by bee08.uspnet.usp.br (8.6.8.1/RISC-CCE2.0) id KAA20405 Received: from localhost (szeinfel@localhost) by fox.cce.usp.br (8.6.4/CONVEX120-CCE2.0) id KAA08733 Date: Mon, 30 May 1994 10:24:30 -0300 (BDT) From: Rafael N Szeinfeld Subject: hyperchem. To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLnetter's, I would like to know if hyperchem is useful for research purpouses that is if it is used for research pupouses (is it powerful enough ?), a mesure of this may be references using hyperchem, so if you know some please let me know. Thank's in advance. Rafael Najmanovich From Patrick.Bultinck@rug.ac.be Mon May 30 09:53:00 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id IAA07122; Mon, 30 May 1994 08:58:13 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA08986 (5.67b/IDA-1.5 for ); Mon, 30 May 1994 14:57:33 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA15599; Mon, 30 May 94 14:54:35 +0200 Date: Mon, 30 May 1994 14:54:30 +0200 (MET DST) From: Patrick Bultinck Subject: Summary on optimization To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 3389 Original message (mine)... Dear netters, As you may have seen in my other message, I have sent an appendix to the summary on the use of symmetry in optimizations of molecular geometries. As became clear soon after I sent my original question there is no real conclusive answer that is superb to another. Another thing I would like to know, since I have to do quite some extensive optimizations is on the use of the initial Hessian. As most of you will know there is a big dependance for the number of required steps in an optimization (and so CPU-time) on the value of the initial Hessian (energy second derivative matrix). This is pointed out by e.g. Schlegel in Ab Initio methods in Quantum Chemistry, p 249 in Advances in chemical physics, LXVII (1987) p.249. He states (and this will be no suprise for you) that "an accurate initial estimate initial estimmate of the second derivative matrix can improve the rate of convergence significantly ...". Now what better initial Hessian than the one computed analytically or numerically for the starting geometry. Another possibility would be to use the one calculated at a lower level (of theory or basis set). This is possible through the fact that hessians are always 3N*3N (N=number af atoms). Another widely used one is to use some sort of positive diagonal matrix that will be updated during the optimization, so that the number of steps is exceeded significantly, but no initial hessian has to be calculated. My question is simple, What is the opinion of the more experienced quantum chemists on the use of different approaches to find an initial hessian ? (a summary will be sent, so that all netters can hear all sorts of opinions... like last time) Are there any simple rules of thumb that will approximately tell you what will be the relative time needed for the computation of the Hessian relative towards the number of steps it will require to find a half-good initial Hessian starting from e.g. a positive definite diagonal matrix ? (given basis set and number of atoms). Patrick, University of Ghent, Belgium. From: David Heisterberg I'm not one of your more experienced quantum chemists, but I've always had much better luck when an analytical hessian was available. Note that a diagonal initial guess hessian is basically equivalent to using steepest descent on the first few steps. Anyway, if a lower level of theory gives a reasonably good geometry, it will probably give a reasonably good hessian (but then I'm of prussian descent, so what would I know?). -- David J. Heisterberg (djh@ccl.net) Gee, it's so beautiful, I gotta The Ohio Supercomputer Center give somebody a sock in the jaw. Columbus, Ohio -- Little Skippy (Percy Crosby) From: schuetz@ips.id.ethz.ch (Martin Schuetz) Well, there was a paper in JPC where the convergence for several initial Hessian matrices were compared and an empirical formula to generate an initial Hessin was proposed. The reference is: T.H. Fischer and J. Almloef, JPC 96, 9768 (1992) With best regards M.Schuetz -- Martin G. Schuetz, Ph.D. Phone: +41 1 632 57 82 Interdisciplinary Project Center FAX: +41 1 261 04 68 for Supercomputing, ETH Zuerich Switzerland E-mail: schuetz@ips.id.ethz.ch or mgs@ips.id.ethz.ch From chuck@iaccess.cstat.co.za Mon May 30 18:42:33 1994 Received: from mickey.iaccess.za for chuck@iaccess.cstat.co.za by www.ccl.net (8.6.4/930601.1506) id SAA12316; Mon, 30 May 1994 18:02:38 -0400 Received: from slipper225.cstat.co.za by mickey.iaccess.za with smtp (Smail3.1.28.1 #1) id m0q8FPP-0004MtC; Tue, 31 May 94 00:02 GMT+0200 Message-Id: From: "Charles Marais" To: chemistry@ccl.net Date: Mon, 30 May 1994 23:53:12 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Low cost Stereo viewing glasses Reply-to: chuck@iaccess.cstat.co.za Priority: normal X-mailer: Pegasus Mail/Windows (v1.11a) > Of critical importance is whether software will support these glasses. > Does anyone know of such developments? At <$100 per system, > is this form of 3D viewing likely to take off in chemistry? Without a doubt. I've been waiting for this for a long time - recently, someone wrote a letter in Dr Dobbs Journal about such glasses and included an extremely simple schematic for driving them from the serial port ! (so they'd have be alble to switch with about 12 V), but I couldn't find the glasses. I think that if they were freely available, software will appear within a month. ---------------------------------------------------------------------------------------- Charles Marais Phone 27-21-788-2248 Southern Scientific Fax 27-21-788-6613 17 Capri Rd Email Chuck@iaccess.cstat.co.za St James Chuck@psipsy.uct.ac.za South Africa 7700 -----------------------------------------------------------------------------------------