From ccl@www.ccl.net Fri Apr 11 11:52:24 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA05182; Fri, 11 Apr 1997 10:52:23 -0400 (EDT) Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by bedrock.ccl.net (8.8.3/950822.1) id KAA13136; Fri, 11 Apr 1997 10:52:23 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id KAA08804; Fri, 11 Apr 1997 10:52:24 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA15995; Fri, 11 Apr 1997 10:52:16 -0400 Date: Fri, 11 Apr 1997 10:52:12 -0400 (EDT) To: Joachim Schummer Cc: chemistry@ccl.net Subject: Re: CCL:Philosophy of Chemistry Journal In-Reply-To: <334AF8F5.2072@geist-soz.uni-karlsruhe.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Schummer: I am very glad to know this site of dicussion about philosophy of chemistry. I have a web page of my dissertation with a chapter of "philosophy of computational quantum chemistry. The address is: http://alphanla.chem.uga.edu/~buyong/philo/philo.html ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Tue, 8 Apr 1997, Joachim Schummer wrote: > > Journal Announcement "Philosophy of Chemistry"! > > The former Bulletin of the German Working Group "Philosophy and > Chemistry" has been extended to an online journal published at the > University of Karlsruhe, Germany: > > HYLE. An International Journal for the Philosophy of Chemistry > http://www.uni-karlsruhe.de/~philosophie/hyle.html > > HYLE is dedicated to all philosophical aspects of chemistry. Detailed > informations concerning scientific concept, subscription, and > contributing to HYLE are available on the homepage. > The former issues (1.1995, 2.1996) as well as a preview of 3.1997 are > available. > There is also a Collected Bibliography "Philosophy of Chemistry" (more > than 1500 titles!) including articles on the history of theories, ideas, > and concepts of chemistry. > Web sites containing related links, new publications, and current > activities in the philosophy of chemistry are in progress. (Please mail > anything of interest to me). > > Regards, > Joachim Schummer > > > ------------------------------------------------------------ > Dr. Joachim Schummer > Institute of Philosophy, University of Karlsruhe > Postfach 69 80, D-76128 Karlsruhe, GERMANY > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From bernhold@npac.syr.edu Fri Apr 11 16:35:35 1997 Received: from postoffice.npac.syr.edu for bernhold@npac.syr.edu by www.ccl.net (8.8.3/950822.1) id PAA07491; Fri, 11 Apr 1997 15:52:20 -0400 (EDT) Received: from columbia (columbia.npac.syr.edu [128.230.14.61]) by postoffice.npac.syr.edu (8.7.5/8.7.1) with SMTP id PAA29576; Fri, 11 Apr 1997 15:52:21 -0400 (EDT) Message-Id: <9704111946.AA18136@columbia> Received: by columbia (AIX 4.1/UCB 5.64/N-0.12) id AA18136; Fri, 11 Apr 1997 15:46:14 -0400 To: chemistry@www.ccl.net Cc: bernhold@npac.syr.edu Reply-To: bernhold@npac.syr.edu Subject: Chemistry Software and Information Resources (CSIR) Date: Fri, 11 Apr 1997 15:46:14 -0400 From: "\"David E. Bernholdt\" <\"David E. Bernholdt\"" We are pleased to announce a new web-based service... Chemistry Software and Information Resources http://www.csir.org CSIR (pronounced caesar) is an information resource for chemistry software, its development, and its use (in the broadest sense). It brings together a great deal of information scattered across the Internet, often hard to find and use, and makes it easily available to anyone with a web browser, at no charge. -------- FEATURES -------- * Chemistry Software Exchange -- A catalog of commercial and non-commercial software for chemists. Includes links to software available on the Internet, and contact info for commercial offerings. Submissions welcome. * AskNPAC Chemistry Mailing List Archive -- Browse or search a large selection of chemistry-related mailing lists and newsgroups. Search any combination of lists for mail header (sender, date, etc.), URLs, or general text. * Links to other chemistry software information (coming soon). ----------------------------------------- PUBLICATIONS AND PRESENTATIONS ABOUT CSIR ----------------------------------------- * Poster COMP 193 at ACS meeting in San Francisco, at Sci-Mix session (Monday 8pm, Moscone Center, Exhibit Hall D), and COMP session (Tuesday 7pm, San Francisco Marriott, Salon 7, Lower B-2 Level) * Trends in Analytical Chemistry article at http://www.elsevier.nl/inca/homepage/saa/trac/resource.htm (also to appear in print version of TrAC) ---------------------- INTERNET ACCESS POINTS ---------------------- CSIR home page: http://www.csir.org CSIR Software Exchange Submissions: http://www.csir/org/catalog/chemistry/contribute.html Comments and suggestions to: chemistry_maintainers@nhse.org ---------------- MORE INFORMATION ---------------- Chemistry Software Exchange Right now we have about 140 software packages cataloged in the repository. That's clearly that's just a fraction of what's out there, and what we do have now is pretty cursory -- meant to give people the idea of what we're intending to do. We'd like to make this "the" resource for anyone looking for chemistry-related software, so we need your help to expand our holdings. If you're a software developer, please submit your software to CSIR. If you're a software user, tell us about your favorite packages (with as much contact information as you can provide on the supplier). The web pages have forms with the information we need. We want to keep the catalog information technical rather than ad material. Catalog entries can include contact information links to your own web site where you can do whatever advertising you please. Also for software developers: we can act as an additional distribution point or archive location for your software. AskNPAC Chemistry Mailing List Archive The idea here is to collect in a single place a rather substantial body of information about chemistry-related software, its use, and about chemistry in general which is presently widely scattered across the Internet. In this way, we hope to make it easier to find and use. CSIR subscribes to more than 90 mailing lists, of which 60 appear to be active. We have more than 75,000 messages in the archive, representing the better part of a year's worth of traffic. Soon we will be adding "back issues" of mailing lists, where they are available. Information is available on all of the lists CSIR subscribes to, and if you're aware of anything we don't carry we'd love to hear about it. Relationship to Existing Resources CSIR's goal is to make existing resources easier to find and use, not to compete with them. Software developers can only benefit from listing their software in the catalog, where others might discover it suits their needs. We _can_ act as an additional distribution point for software, but it is not necessary in order to have a catalog listing. Similarly for mailing lists, we merely make it easier for readers to access existing mailing lists. We do not encourage non-subscribers to post to lists, and CSIR itself provides no mechanism to do so. We do provide complete information about how to subscribe to every list in the archive. CSIR is a free service, brought to you by the Northeast Parallel Architectures Center (http://www.npac.syr.edu) at Syracuse University and the National HPCC Software Exchange (http://www.nhse.org). We welcome your feedback on the service and ideas for improvement. NOTE: If your web browser complains that www.csir.org "does not have a DNS entry" or "was not found" (as opposed to "did not respond"), it may be because the browser was too impatient to wait for the DNS lookup to complete (csir.org is relatively new and probably is not widely cached in DNS servers yet). Often if you try exactly the same URL again, it will be successful. This "trick" applies to many relatively new sites, not just CSIR. Best regards, David Bernholdt, for the CSIR project chemistry_maintainers@nhse.org From jstewart@iti2.net Fri Apr 11 21:35:35 1997 Received: from cougar.iti2.net for jstewart@iti2.net by www.ccl.net (8.8.3/950822.1) id UAA08603; Fri, 11 Apr 1997 20:57:52 -0400 (EDT) Received: from gj1-15.iti2.net (gj1-15.iti2.net [208.141.145.15]) by cougar.iti2.net (8.8.5/8.7.3) with SMTP id SAA20385 for ; Fri, 11 Apr 1997 18:59:52 -0600 Message-Id: <3.0.16.19691231170000.2d7fec12@iti2.net> X-Sender: jstewart@iti2.net (Unverified) X-Mailer: Windows Eudora Pro Version 3.0 (16) Date: Fri, 11 Apr 1997 17:57:46 -0600 To: CHEMISTRY@www.ccl.net From: "James J. P. Stewart" Subject: Analytical CI gradients in semiempirical programs Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To reply again re Dr Pachkovsky's observations: The "stationary point" he reports yields a heat of formation of 178.33025 kcal/mol and a gradient norm of over 1 kcal/mol/A. Geometry optimization results in a similar geometry, reported by me earlier, with a H.o.F. of 178.32945, and a gradient norm of 0.09 kcal/mol/A. The geometry at 178.33025 kcal/mol is not a stationary point, for two reasons. First, it is 0.0008 kcal/mol above the nearby "stationary point", and second, as Dr Pachkovsky points out, the "stationary point" is, in fact, a hilltop. The difference in energy of the two geometries is reponsible for the large GNORM reported by Dr Pachkovsky. When I attempted to reduce the GNORM below 0.09 kcal/mol/A, the geometry changed so as to lower the energy by a few tens of kcal/mol. That the active space is incomplete can readily be shown by rerunning the job with C.I.=4. This results in a large decrease in energy. Dr Pachkovsky is correct in that the space is "complete" as far as CI and gradient calculations are concerned, but because the effect of increasing the size of the active space has a profound effect on the results, the calculation is as useful as a single point calculation on an arbitary geometry. The fact that the gradient could be lowered to less than 0.1, in accordance with Dr Pachkovsky's criterion, demonstrates the falsity of the statement "This is not a legitimate reason for a breakdown of analytical gradients." Now to the program itself. Dr Pachkovsky's data set contains the keyword PLCRT=0.0000001, which is not a keyword of MOPAC 93 or MOPAC 7. This suggests that the program being used by Dr Pachkovsky was modified after it was received from QCPE. While MOPAC 93, Revision 2 is, as Dr Pachkovsky suggests, the "latest and greatest", it is not invulnerable to damage caused by changing the source code. This might be the reason for the differences in results. In case there is any doubt about the validity of Liotard's analytical derivative method, here is a re-calculation of Dr Pachkovsky's system in which the system is constrained to be planar. Users of MOPAC 93, Revision 2, are invited to repeat this calculation. And now that I am heading off to San Francisco, I beg leave to back out of any further discussion on this topic. Jimmy Stewart SUMMARY OF MNDO CALCULATION MOPAC 98.00 C6 H6 Fri Apr 11 18:40:14 1997 1SCF GRAD C.I.=2 ROOT=3 SINGLET PRECISE & T=1000000 MECI 1SCF WAS SPECIFIED, SO BFGS WAS NOT USED SCF FIELD WAS ACHIEVED HEAT OF FORMATION = 178.329472 KCAL = 746.13051 KJ ELECTRONIC ENERGY = -3211.052760 EV STATE: SINGLET Ag CORE-CORE REPULSION = 2366.325464 EV GRADIENT NORM = 0.000567 DIPOLE = 0.00000 DEBYE SYMMETRY: D2h NO. OF FILLED LEVELS = 15 CONFIGURATION INTERACTION WAS USED IONIZATION POTENTIAL = 8.654580 EV MOLECULAR WEIGHT = 78.113 SCF CALCULATIONS = 1 COMPUTATION TIME = 0.413 SECONDS FINAL GEOMETRY OBTAINED CHARGE 1SCF GRAD C.I.=2 ROOT=3 SINGLET PRECISE & T=1000000 MECI C 0.00000000 0 0.0000000 0 0.0000000 0 0 0 0 -0.0603 C 1.38675637 1 0.0000000 0 0.0000000 0 1 0 0 -0.0609 C 1.54669847 1 119.6677872 1 0.0000000 0 2 1 0 -0.0609 C 1.38675161 1 119.6677106 1 0.0000000 0 3 2 1 -0.0603 C 1.38675663 1 120.6645001 1 0.0000000 0 4 3 2 -0.0609 C 1.38675212 1 120.6645308 1 0.0000000 0 1 2 3 -0.0609 H 1.09300947 1 119.6675465 1 180.0000000 0 1 2 3 0.0580 H 1.08399943 1 123.4960132 1 180.0000000 0 2 1 3 0.0621 H 1.08399997 1 116.8360371 1 -180.0000000 0 3 2 1 0.0621 H 1.09300943 1 119.6680004 1 180.0000000 0 4 3 2 0.0580 H 1.08399948 1 123.4959112 1 180.0000000 0 5 4 3 0.0621 H 1.08399988 1 123.4962036 1 180.0000000 0 6 1 2 0.0621