From upolklan@savba.savba.sk Thu Jun 2 07:43:16 1994 Received: from savba.savba.sk for upolklan@savba.savba.sk by www.ccl.net (8.6.4/930601.1506) id HAA18747; Thu, 2 Jun 1994 07:20:00 -0400 Received: by savba.savba.sk id AA00307 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Thu, 2 Jun 1994 13:21:28 +0200 From: Angela Kleinova Message-Id: <199406021121.AA00307@savba.savba.sk> Subject: C20..C540 energies linear? To: chemistry@ccl.net Date: Thu, 2 Jun 1994 13:21:27 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL5] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1205 dear CCL netters, ----------------- sorry to trouble you, but: in the recent article bakowies & thiel (JACS vol.113, p.3704 (1991)) calculated MNDO energies (or heats of formation) up to the C(540) carbon cluster, starting from C(20) (as far as I remember). Dependence: delta_H_subscript_f = a*N + b where N is # of carbon atoms, is almost linear. But why the b is not zero? thanX for all who reply to me ;-) +-----------------------------------------------------------------------+ + Angela Kleinova + + Polymer Institute + + Slovak Academy of Sciences Tel: ++42 +7 378 2252 + + Dubravska cesta 9, 842 28 Bratislava Fax: ++42 +7 378 2192 + + Slovak Republic E-mail: upolklan@savba.sk + + EUROPE + +-----------------------------------------------------------------------+ ,,, (o o) +-----------------------------oOO--(_)--OOo-----------------------------+ + And all this science I don't understand, it's just my work for 5 days + + a week ... +-----------------------------------------------------------------------+ From jborn@triton.unm.edu Thu Jun 2 10:43:20 1994 Received: from triton.unm.edu for jborn@triton.unm.edu by www.ccl.net (8.6.4/930601.1506) id KAA29415; Thu, 2 Jun 1994 10:39:23 -0400 From: Received: by triton.unm.edu (Smail3.1.28.1 #5) id m0q9DvV-0001CnC; Thu, 2 Jun 94 08:39 MDT Message-Id: Subject: H-bonding in alphahydroxyesters To: CHEMISTRY@ccl.net Date: Thu, 2 Jun 1994 08:39:21 -0600 (MDT) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 437 dear CCL netters I am interested in modeling hydorgen bonding in alpha-hydroxy esters to help in the evaluation of the rate of hydrolysis of compounds of this type. I would like to start with alpha hydroxy methylacetate.. I have attempted to utilize the MM+ option in Hyperchem with out success. Suggestions for methods and/or procedures would be greatly appreciated. Thanks Jerry L. Born Professor of Pharmacy jborn@triton.unm.edu From hodgkina@vax.ox.ac.uk Thu Jun 2 11:43:19 1994 Received: from oxmail2.ox.ac.uk for hodgkina@vax.ox.ac.uk by www.ccl.net (8.6.4/930601.1506) id LAA01211; Thu, 2 Jun 1994 11:17:43 -0400 From: Received: from vax.ox.ac.uk by oxmail2.ox.ac.uk. with SMTP (PP) id <24256-0@oxmail2.ox.ac.uk.>; Thu, 2 Jun 1994 16:15:05 +0100 Received: by vax.ox.ac.uk (MX V4.0-1 VAX) id 40; Thu, 02 Jun 1994 16:14:09 +0100 Sender: hodgkina@vax.ox.ac.uk Date: Thu, 02 Jun 1994 16:14:08 +0100 To: CHEMISTRY@ccl.net Message-ID: <0097F5BA.E1BFADAD.40@vax.ox.ac.uk> Subject: re Mol2Mol beta-testers Dear Netters I have been overwhelmed by your 50+ kind offers to beta-test our Mol2Mol file translation program. I will not be able to reply to the messages individually. A few general points. (1) We do not expect there to be a version for SGI, UNIX, VAX or the Mac in the near future. (2) We do not expect the program to support formats other than those listed in my original posting - but there was no consensus on additional formats suggested in the e-mail that I received. (3) A couple of replies mentioned Babel as a competitor but the programs are very different in feel and my expectation is that they will not be competitors since the formats they cover do not hugely overlap. Please no more offers to beta-test. If you want to receive details on the program when it is available I will be pleased to keep you posted and everyone who has responded to my request will be informed of publication details later in the year. The size of the response to my request suggests that this List is a very important resource for chemists with computing interests. Thanks to the community that sustains it. Best wishes Adam Hodgkin Cherwell Scientific The Magdalen Centre Oxford Science Park Oxford OX4 4GA Tel: 44-865-784800 Fax: 44-865-784801 adam.hodgkin@queens.oxford.ac.uk From MSCHRIVER@kean.ucs.mun.ca Thu Jun 2 13:43:24 1994 Received: from morgan.ucs.mun.ca for MSCHRIVER@kean.ucs.mun.ca by www.ccl.net (8.6.4/930601.1506) id MAA04905; Thu, 2 Jun 1994 12:44:53 -0400 Received: from leif.ucs.mun.ca by morgan.ucs.mun.ca with SMTP id AA05605 (5.65d3+/IDA-1.4.2+MUN1.3 for chemistry@ccl.net); Thu, 2 Jun 94 14:16:25 -0230 Date: Thu, 2 Jun 1994 14:14:31 +0200 (IST) From: "Schriver,M;Chemistry;" Subject: CCL:Hyperchem To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hey out there, I have appreciated the repsonses that I have been getting on the HypeChem issue. It is clear from the reponses that I have received that the semi-empirical programs in the HyperChem suite are fully functional and have not been truncated. That is reassuring and I will make a point of mentioning that to the chemists who were telling me there were problems with HyperChem. Of the comments that I have had both through the list and by personal messages it is clear that HyperChem has an exceptional ability to generate graphics and build molecules. I am going to keep my copy of HyperChem. As far as the other issue .. ie "where can you use semi-empirical calculations?" I can see that I wandered into an area between two entrenched armies. Is there a FAQ somewhere where the "experts" have fought this issue out? What it boils down to for me is wether I can use AM1 or PM3 to calculate the orbitals of a heterocycle that contains S and/or P. I have appreciated the help. Mel Schriver P.S. Ghislain, I would not have posted my concern if it had have been just our conversation. I in fact had several similar conversations over several months. Glad you enjoyed the discussion tho ;-) From MSCHRIVER@kean.ucs.mun.ca Thu Jun 2 14:47:25 1994 Received: from morgan.ucs.mun.ca for MSCHRIVER@kean.ucs.mun.ca by www.ccl.net (8.6.4/930601.1506) id OAA25383; Thu, 2 Jun 1994 14:41:57 -0400 Received: from leif.ucs.mun.ca by morgan.ucs.mun.ca with SMTP id AA18593 (5.65d3+/IDA-1.4.2+MUN1.3 for chemistry@ccl.net); Thu, 2 Jun 94 16:13:29 -0230 Date: Thu, 2 Jun 1994 16:11:34 +0200 (IST) From: "Schriver,M;Chemistry;" Subject: Re: HyperChem (fwd) To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am going to forward this letter to the CCL because it directly deals with the questions that I asked. It also provides a couple of good refs on the methods. Mel S. ***************** forwarded mail ************************** Dear Dr. Schriver, I read your message about your application of HyperChem. I think, before applying MOBY, or HyperChem, or similar programs, the user should at least read a book on semiempirical methods, their potential and their pitfalls, and how to check the reliability of the results from those programs. Two of those books were also published by Springer-Verlag, I attach information on these books. (Available from Springer-Verlag New York, Inc.) Sincerely yours Rainer Stumpe Sciences Editorial Springer-Verlag Tiergartenstr. 17 D-69121 Heidelberg Phone: +49-(0)6221-487 310 Fax: +49-(0)6221-487 139 Internet: Stumpe@spint.compuserve.com ------------------------------------------------------------- V.I. Minkin, B.Ya. Simkin, R.M. Minyaev, Rostov University, Rostov, USSR Quantum Chemistry of Organic Compounds Mechanisms of Reactions 1990. XV, 270 pp. 66 figs. 35 tabs. Hardcover DM 148,- ISBN 3- 540-52530-0 This textbook on the application of ab initio and semiempirical techniques for the analysis of organic reaction mechanisms is designed for chemistry undergraduates. The material is presented according to the mechanistic types: nucleophilic and electrophilic substitution, addition reactions, radical, pericyclic, proton and electron transfer reactions. Orbital and electrostatic models are used for structural correlations of interacting molecular systems along the reaction paths. Particular attention is focussed on the characteristics of the transition state. The text combines phenomenology with the basic theoretical principles needed to understand and predict chemical reactivity. -------------------------------------------------------------- B.O. Roos, University of Lund, Sweden (Ed.) Lecture Notes in Quantum Chemistry European Summer School in Quantum Chemistry With contributions by numerous experts 1992. VIII, 421 pp. 13 figs. 23 tabs. (Lecture Notes in Chemistry. Vol. 58) Softcover DM 118,- ISBN 3-540-55371-1 Quantum Chemistry is the course material of a European Summer School in Quantum Chemistry, organized by Bjrn O. Roos. It consists of lectures by outstanding scientists who participate in the education of students and young scientists. The book has a wider appeal as additional reading for University courses. Contents: P.-A. Malmquist, Lund, Sweden: Mathematical Tools in Quantum Chemistry.- J. Olsen, Lund, Sweden: The Method of Second Quantization.- P.R. Taylor, Moffet Field, CA: Molecular Symmetry and Quantum Chemistry.- B.O. Roos, Lund, Sweden: The Multiconfigurational (MC) Self-Consistent Field (SCF) Theory.- P.E.M. Siegbahn, Stockholm, Sweden: The Configuration Interaction Method.- T. Helgaker, Oslo, Norway: Optimization of Minima and Saddle Points.- P.R. Taylor, Moffet Field, CA: Accurate Calculations and Calibration.- U. Wahlgren, Stockholm, Sweden: Effective Core Potential Method. Computational chemistry has today reached a status where available methods and program systems are also used by scientists who are not specialists in the field. As a result there is a growing need to acquire the background knowledge necessary for a skilful use of these methods. This book will be useful as a textbook for students and researchers interested in learning more about modern methodology in quantum chemistry. From ABRASH@urvax.urich.edu Thu Jun 2 16:43:33 1994 Received: from urvax.urich.edu for ABRASH@urvax.urich.edu by www.ccl.net (8.6.4/930601.1506) id QAA14370; Thu, 2 Jun 1994 16:01:57 -0400 From: Received: from urvax.urich.edu by urvax.urich.edu (PMDF V4.3-7 #4834) id <01HD2M2L99BK000E4C@urvax.urich.edu>; Thu, 2 Jun 1994 16:01:10 EDT Date: Thu, 02 Jun 1994 16:01:09 -0400 (EDT) Subject: NH3 Inversion Doubling To: Chemistry@ccl.net Message-id: <01HD2M2LBEHE000E4C@urvax.urich.edu> X-VMS-To: IN%"Chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I would like to add a segment to a physical chemistry lab on the infrared spectrum of ammonia in which students calculate an ab initio potential for the umbrella mode, and then calculate the infrared spectrum of the molecule from the potential (semi-empirical would be ok). What is the lowest level of theory (i.e. the cheapest), which will yield reasonable numbers (i.e., within 10%) for NH3 normal modes, and for the inversion doubling. Sam Abrash Abrash@URVAX.URiCh.EDU From topper@magnum.cooper.edu Thu Jun 2 18:43:23 1994 Received: from magnum.cooper.edu for topper@magnum.cooper.edu by www.ccl.net (8.6.4/930601.1506) id SAA16080; Thu, 2 Jun 1994 18:23:30 -0400 Received: by magnum.cooper.edu id AA05027 (5.65c/IDA-1.4.4 for Chemistry@ccl.net); Thu, 2 Jun 1994 18:24:39 -0400 Date: Thu, 2 Jun 1994 18:24:39 -0400 From: Robert_Topper Message-Id: <199406022224.AA05027@magnum.cooper.edu> To: ABRASH@urvax.urich.edu, Chemistry@ccl.net Subject: Re: CCL:NH3 Inversion Doubling On this topic I can provide no concrete advice other than to have a look at the following paper: "reaction path power series analysis of NH3 inversion," by R. Steckler and D.G. Truhlar, J. Chem. Phys. 93, 6570 (1990). In this paper it is noted that the inversion barrier height is quite sensitive to the number of basis functions used. This may be a useful starting point towards answering your question. -rqt ************************************************************************ Prof. Robert Q. Topper internet: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 Cooper Square subway: take the N/R to 8th/NYU New York, NY 10003 USA or the 6 to Astor Place The Cooper Union for the Advancement of Science and Art, established by Peter Cooper in 1859, is a private institution of higher learning where all students receive full-tuition scholarships. ************************************************************************ From slee@hyper.hyper.com Thu Jun 2 18:52:12 1994 Received: from seraph.uunet.ca for slee@hyper.hyper.com by www.ccl.net (8.6.4/930601.1506) id RAA15719; Thu, 2 Jun 1994 17:44:01 -0400 Received: from hyper by mail.uunet.ca with UUCP id <99951-5>; Thu, 2 Jun 1994 17:43:36 -0400 Received: by hyper.hyper.com.hyper.com (931110.SGI/890607.SGI) (for ccl.net!chemistry) id AA04417; Thu, 2 Jun 94 14:06:55 -0400 From: slee@hyper.hyper.com (Thomas Slee) Message-Id: <9406021806.AA04417@hyper.hyper.com.hyper.com> Subject: Re: HyperChem To: chemistry@ccl.net Date: Thu, 2 Jun 1994 14:06:54 -0400 X-Mailer: ELM [version 2.3 PL9] Dear CCL readers, Declaration of interest: I work for Hypercube, developers of HyperChem. It seems appropriate, with the current round of discussion of HyperChem experiences going on, that I do two things: 1. Avoid unnecessary interference in this discussion, as an interested party, but: 2. Update and correct purely factual observations where necessary. With this in mind, here is an update on Dr. Bliznyuk's comments, which referred to Release 3 of HyperChem. The current release is Release 4. | | Last year we had a chance to try HyperChem v 3.0. This program has | good graphics and very good molecular editor/builder. | Thank you! (couldn't resist leaving it in there). | | Unfortunately, it is very slow, at least for semiempirical calculations. | For example, it takes 35 min. on 486DX2 50MHz with 16 MB of memory to do | MNDO 1SCF and gradients for C60 (compare to Sibiq - 10 min.). | Dr. Bliznyuk will be happy to know we have significantly improved the performance of this kind of calculation. Calculations on a 486DX2 50 MHz with 20MB of memory show the following: (C_60, AM1, SCF convergence to 1e-4 kcal/mol, + gradient evaluation), HyperChem Release 3. 33 min (my calculation) HyperChem Release 3. 35 min (Dr. Bliznyuk's calculation) Sibiq 10 min (Dr. Bliznyuk's calculation) HyperChem Release 4. 7 min 30 sec. (my calculation.) C_60 is a very memory-intensive system for HyperChem's analytical energy derivative computation. Hence some of this time is taken up with disk access (I suspect this is the cause of the 2 min discrepancy between the Release 3 calculations). For a system with the same number of atomic orbitals but more hydrogen atoms (C_40H_80) the memory requirements go down by 3Mb and the Release 4 time for SCF plus gradient becomes 6 min 30 sec. I have no data from Sibiq for this system, as we don't have that program in house. We did do a couple of small calculations checking a demo disk (small molecules only) of Sibiq against HyperChem and the results came out for C6H10 that HyperChem takes 3.0 seconds for this small system, while Sibiq takes 5.3 sec. Please do not take this as a claim for superior performance overall for HyperChem compared to Sibiq; it is quite possible that in other calculations Sibiq would be faster than HyperChem. It is certainly not my intent to compare the two programs, merely to show that the timings I give are consistent with Dr. Bliznyuk's values, and that we have indeed speeded up the program significantly. On the subject of timings, we have carried out test calculations similar to the above on a couple of different platforms comparing HyperChem and MOPAC 6. Depending on molecule and compiler, sometimes MOPAC is faster, sometimes HyperChem. The other point on which I wish to reassure CCL readers is the implicit suggestion in an earlier posting that HyperChem may give results inconsistent with MOPAC or AMPAC for NDDO-type calculations. Our formal testing of HyperChem involves over 1,000 separate calculations. This testing, and two years of customer experience with the program, have yet to show a case where HyperChem and MOPAC produce different results for the same calculation. The insignificant differences mentioned by Antti Poso come, we believe, from MOPAC 6's slightly inconsistent values for conversion factors in different parts of the program. Tom Slee -- Tom Slee, Hypercube Inc., 419 Phillip St., Waterloo, Ont., Canada, N2L 3X2 E-Mail: slee@hyper.com, Tel. (519)725-4040, Fax. (519)725-5193. From ostlund@hyper.hyper.com Thu Jun 2 23:43:26 1994 Received: from seraph.uunet.ca for ostlund@hyper.hyper.com by www.ccl.net (8.6.4/930601.1506) id XAA18036; Thu, 2 Jun 1994 23:22:10 -0400 Received: from hyper by mail.uunet.ca with UUCP id <119522-2>; Thu, 2 Jun 1994 23:21:49 -0400 Received: by hyper.hyper.com.hyper.com (931110.SGI/890607.SGI) (for ccl.net!chemistry) id AA06655; Thu, 2 Jun 94 23:26:48 -0400 Date: Thu, 2 Jun 1994 23:26:48 -0400 From: ostlund@hyper.hyper.com (Neil S. Ostlund) Message-Id: <9406030326.AA06655@hyper.hyper.com.hyper.com> To: chemistry@ccl.net Subject: Parallelism and HyperChem It appears that we have beat the HyperChem reliability and performance issues into the ground but the discussion raises an interesting issue that I thought might be worth commenting on. It has to do with parallel processing and might make an interesting anecdote for an audience like this. I talked about it at the Grand Challenge Parallel Processing Conference in Baton Rouge in February but did not have time to write a paper for the proceedings. The semi-empirical calculations of Release 4 of HyperChem are very much faster than those of HyperChem Release 3 which are very much faster than those of Release 2. A principal reason is that we have been going through a process here, to make HyperChem go faster, that we might call "Serialization" as opposed to "Parallelization". Yufei Guo here at Hypercube is now one of the world's experts at getting rid of parallelism! <:) The semi-empirical calculations of HyperChem started out life many years ago in purely parallel form, running originally on Intel's Hypercube machines (note the name of our company). The first PC version of HyperChem's semi-empirical calculations were essentially these parallel codes with disjoint-memory message passing being replaced by a simple memory copy operation. Now, most people in parallel processing like to show speed-up curves with performance relative to the parallel program on 1 processor. But, as we all know, parallelism comes at a cost and a parallel program has an overhead such that it may not perform well on one processor compared to an optimized serial program. Over the last couple of years as we have optimized the performance of HyperChem and "Serialized" it, we have gotten very significant speed improvements. We may not have the best optimizers yet - these mainly derive still from methods where parallel processing algorithms were available. These issues indicate some of the problems with parallel processing that are partially responsible for slowing its acceptance into the mainstream. They also show some of the problems for developers like us who would like to have optimum performance all the way from laptops to supercomputers. The parallelism in semi-empirical codes can give rise to many issues about performance but one of the simplest issues is just the efficiency of parallel matrix diagonalization. We got a significant improvement in HyperChem by replacing our parallel diagonalizers, which we used to think of as quite good, with the very best serial diagonalizers. On the other hand, we feel that our parallelization in molecular mechanics, using our tractor-tread algorithms, etc. is not costing us very much. On the new Intel Paragon, HyperChem gave a speed up of 31 on 32 processors for a 4096 atom MD run, yet we consider it to also run fast in serial mode. If anyone has molecular mechanics times for HyperChem compared to MSI, Biosym, Tripos, etc., we would certainly find those quite interesting, as might others <:). I apologize if this or my previous posting has any commercial flavor to it. I can't always tell whether I am wearing my CEO hat or my scientist hat. Also, if I sound negative about my old friend, parallel processing, I'm not - its just that like any deep topic there are many different ways of looking at it. Cheers, ------------ Neil Ostlund President, Hypercube Inc. 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: ostlund@hyper.com