From 94970459@tolka.dcu.ie Sun May 11 15:42:31 1997 Received: from tolka.dcu.ie for 94970459@tolka.dcu.ie by www.ccl.net (8.8.3/950822.1) id OAA13862; Sun, 11 May 1997 14:45:42 -0400 (EDT) Received: by tolka.dcu.ie; (5.65v3.2/1.1.8.2/14Feb96-0535PM) id AA29760; Sun, 11 May 1997 19:39:27 +0100 Date: Sun, 11 May 1997 19:39:26 +0100 (BST) From: patrick kane <94970459@tolka.dcu.ie> To: CCL Every , HChem User , HChem Supp Subject: HyperChem, AM1 and Phosphorous-Oxygen Bonds Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, On Page 122 of the HyperChem Computational Chemistry Manual, v. 4.0, it is stated that treatment of phosphorous-oxygen bonds with the AM1 semi-empirical (SE) method is inaccurate. However, I cannot find a reference for this statement. Could someone please point me to an appropriate article. Furthermore, can anyone suggest what is the most appropriate SE method? Thanks in advance for any help. Kind Regards, Paddy. ************************************************************************* * * * Paddy Kane email: 94970459@tolka.dcu.ie * * School of Chemical Sciences * * Dublin City University Tel: 00-353-1-7045641 * * Dublin 9 * * Ireland. Fax: 00-353-1-7045503 * * * ************************************************************************* From Eugene.Leitl@lrz.uni-muenchen.de Sun May 11 17:42:31 1997 Received: from sunsrv5.lrz-muenchen.de for Eugene.Leitl@lrz.uni-muenchen.de by www.ccl.net (8.8.3/950822.1) id RAA14372; Sun, 11 May 1997 17:16:23 -0400 (EDT) Received: from sun4.lrz-muenchen.de by sunsrv5.lrz-muenchen.de; Sun, 11 May 97 23:16:23 +0200 Received: by sun4.lrz-muenchen.de (5.x/SMI-SVR4) id AA03783; Sun, 11 May 1997 23:13:57 +0200 Date: Sun, 11 May 1997 23:13:56 +0200 (MET DST) From: Eugene Leitl X-Sender: ui22204@sun4 To: chemistry Subject: "Nanosystems" debunked? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, currently, I am rereading "Nanosystems" by Erik K. Drexler (Wiley, 1992). For those who are unaware of this book, a quick summary. E. K. Drexler proposes a new class of nanoscale engines capable of autoreplication, built from diamondoids (carbon and otherwise) and operating in hard vacuum by means of (hitherto unprecedented) machine-phase chemistry, which are basically downscaled STM manipulators in nanolithography mode (deploying reactive carbon moieties atom-by-atom at roughly 1*10^6 rate). Though a quick perusal of this book by a chemist or molecular biologist may appear it to be dire nonsense, I am no longer certain it is thus simple. Thus I'm asking for assistance in this forum, as, lacking experimental data, Drexler arguments a great deal from computer runs, as MM2, etc. Basically, there are two distinct domains in the book: the more or less classical chemistry at the tool tip, and large-scale dynamics of nontrivial diamondoid structures of several 10^6 atoms. If anybody has read the book: can simulations at such scales generate any reliable data whatsoever? From a computational chemist point of view, is Drexler at all talking sense? Thanks muchly, Eugene Leitl From Alan.Shusterman@directory.Reed.EDU Sun May 11 20:42:33 1997 Received: from reed.edu for Alan.Shusterman@directory.Reed.EDU by www.ccl.net (8.8.3/950822.1) id TAA15052; Sun, 11 May 1997 19:56:38 -0400 (EDT) Received: from isis.Reed.EDU [134.10.2.1 no identification] by reed.edu (Smail-3.2.0.91 1997-Jan-14 #13) id ; Sun, 11 May 1997 16:56:37 -0700 (PDT) Message-id: <3204440@isis.Reed.EDU> Date: 11 May 97 16:56:57 PDT From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) Subject: Summary: Symmetry Bug To: chemistry@www.ccl.net, sparlist@wavefun.com The following note summarizes replies and answers I received to my question about an apparent symmetry bug in Spartan 4.1. Here is my original post: -------------------------------- I run into the following bug every few weeks: I build a molecule with a certain symmetry (Cs in this case) and optimize its structure with symmetry ON. Then I try to reoptimize its structure with a larger basis set while still using symmetry, but Spartan stops with the following error message: SPARTAN AB INITIO PROGRAM Molecule (C1) and archive (CS) have differenty symmetry. Calculation terminating. Can anyone tell me at what point the molecule adopted C1 symmetry? (The input file and the molecule on the scree both still have CS symmetry). Does anyone have any advice on how to proceed? (I really want to do the larger basis set with symmetry, so I need to convince Spartan that the molecule does have CS symmetry.) Note: transferring the coordinates in the archive (CS) to the input file doesn't help (Spartan already did this automatically when I set up the calculation for the larger basis set). Spartan still thinks the molecule is C1 and the archive is CS. ----------------------- Most of the replies that I received fell into one of two categories: 1. use some other software (sound advice in this case; see below) 2. double-check the coordinates in the input file to make sure they really have the expected symmetry. This turns out not to be important in this case (see below). My own comment on suggestion #2 is that the molecule I began with really did have CS symmetry, so this symmetry was maintained during the initial (small basis set) optimization, and the final geometry stored in the archive file had this symmetry. When I setup a reoptimization with a larger basis set, Spartan automatically copies the symmetric "archive" geometry over the "input" geometry, i.e., it makes a new input file, but the input geometry, though changed, still has CS symmetry. The real problem is that Spartan was failing to recognize an obviously symmetric structure. There is no need to double-check the coordinates (I think). The "solution" to my problem appears to be this: SPARTAN 4.1 DOES NOT USE SYMMETRY IN CALCULATIONS INVOLVING DIFFUSE BASIS FUNCTIONS. I don't know if this is documented anywhere, but it is the source of my trouble - my initial optimization (Cs symmetry) did not use diffuse functions, but the reoptimization did call for diffuse functions. Here is a test that I ran to verify the problem: I built bent HOF. This molecule MUST have CS symmetry because it is a nonlinear triatomic. I saved several identical input files and used each one to start a geometry optimization using a different basis set. The optimizations using standard basis sets (STO-3G, 3-21G(*), 6-31G*, 6-31G**, 6-311G**) all recognized and used the molecule's CS symmetry. The optimizations using diffuse basis sets (3-21+G(*), 6-31+G**, 6-31++G**) all disabled symmetry first and carried out the optimization for a C1 molecule. The same behavior was observed whether the calculations were done in memory or DIRECT. Until this is fixed, Spartan users should realize that optimizations for symmetric molecules using diffuse basis sets cannot be carried out with the apparent symmetry. Also, they cannot be "restarted" using wavefunctions or Hessians derived from nondiffuse (i.e., high symmetry) archives. If user knows in advance that calculations with diffuse functions will be needed, then s/he should either disable symmetry at the outset, or not use the "restart" option when using the diffuse basis sets. My thanks to all who contributed. Alan Shusterman Department of Chemistry Reed College Portland, OR