From ron@ala.fh.huji.ac.il Mon Apr 18 01:29:25 1994 Received: from batata.fh.huji.ac.il for ron@ala.fh.huji.ac.il by www.ccl.net (8.6.4/930601.1506) id BAA12874; Mon, 18 Apr 1994 01:16:43 -0400 Received: from ala.fh.huji.ac.il by batata.fh.huji.ac.il via SMTP (920330.SGI/911001.SGI/930210.fh.huji.ac.il) for chemistry@ccl.net id AA03463; Mon, 18 Apr 94 08:16:20 +0300 Received: by ala.fh.huji.ac.il (920330.SGI/920502.SGI) for chemistry@ccl.net id AA07774; Mon, 18 Apr 94 08:16:18 +0300 Date: Mon, 18 Apr 94 08:16:18 +0300 From: ron@ala.fh.huji.ac.il (Ron Elber) Message-Id: <9404180516.AA07774@ala.fh.huji.ac.il> To: chemistry@ccl.net Subject: public domain molecular dynamics code A bug fix version of the public domain Molecular Dynamics code - MOIL - (version 006.2) can be found in the anonymous ftp sites: 128.248.186.70 and 132.64.96.20 A new feature of MOIL is the inclusion of analytical second derivatives of the empirical energy function. Users interested in update and expansion notices as well as rapid update on bug fixes are requested to contact ron@ala.fh.huji.ac.il Ron Elber From jig@qorg.unizar.es Mon Apr 18 04:29:26 1994 Received: from qorg.unizar.es for jig@qorg.unizar.es by www.ccl.net (8.6.4/930601.1506) id DAA13899; Mon, 18 Apr 1994 03:40:06 -0400 Message-Id: <199404180740.DAA13899@www.ccl.net> Received: by qorg.unizar.es (1.37.109.4/16.2) id AA03223; Mon, 18 Apr 94 09:39:10 GMT From: Jose Ignacio Garcia Subject: Summary of responses. 1,3-dipolar cycloadditions To: chemistry@ccl.net Date: Mon, 18 Apr 94 9:39:06 MET Mailer: Elm [revision: 70.85] Dear netters, Thanks to everyone who replied to my request about semiempirical calculations of 1,3-dipolar cycloadditions. Here is the summary of the responses received. =============================== Original question ============================= Dear netters, I intend to start a study about the reaction between diazomethane and a series of complex dipolarophiles. Given that the important size of these systems, I have planned to use semiempirical methods (AM1 and PM3). I have some references dealing with the use of these type of calculations to locate transition structures in this kind of reactions, but the conclusions seem some controversial. I would acknowledge any ideas or suggestions on this topic. Of course, I will summarize the responses to the net. =============================================================================== Jim Blake wrotes: Carlos Sosa and myself published a paper on the using DFT to locate the transition states of a few 1,3-dipolar cycloadditions. We also compared this to HF and MPx levels of theory. The reference is International journal of quantum chemistry vol 49, 511-526, 1994. Jim =============================================================================== Dave Winkler wrotes: We have not had much success predicting regiochemistry of these types of reactions using semiempirical MO. Please send me summary. Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" =============================================================================== Mike Robb wrotes: We did MC-SCF computations on this reaction in 1987 JACS vol 109 4642-4648 1987 I believe that these are delicate problems because if the competition with a biradical mechanism. Semi-empirical methods will certainly be unreliable. Further SCF cannot describle the biradical path. Mike Robb =============================================================================== Konrad Koehler wrotes: Dear Dr. Ignacio, Thank you for your detailed response to my questions. I now have a much better idea of what you are trying to do. I would agree that > 20 heavy atoms is probably too large a problem to handle with ab initio theory, even with a relatively fast workstation. As far as the reaction mechanism of dipolar cycloaddition reactions, this of course goes back to the argument between Firestone and Huisgen. The former argued in favor a stepwise mechanism while Huisgen and most others argue in favor of concerted, asynchronous reaction. Most of the experimental evidence favors the concerted reaction (stereoslectivity of reactions, relatively small rate enhancement with increasing solvent polarity, etc.). I don't have these references at my finger tips, but could pull them out if you are interested. If you are specifically interested in the reaction mechanism, in my opinion, ab initio calculations are the only way to go. If you can't model the full structures of your reactants with ab initio theory, use a model system. If you are interested in the face (i.e., stereo) selectivity question, especially for large systems, perhaps a molecular mechanics approach is worth trying. The strategy is to obtain a transition state geometry at a high level of ab initio theory, and then use this transition state structure to parameterize a force field using special atom types for the atoms directly involved in bond formation/breakage so that the transition state becomes a minimum on the molecular mechanics potential energy surface. Houk and others have shown that it is possible to predict the stereochemical outcome of certain cycloaddition reactions using this approach (for a review see [1]), although this technique has been criticized by Menger.[2,3] Finally enhancements to recent versions of the MacroModel program have [4] been made so that it is relatively easy to set up (although it is non-trivial to parameterize) molecular mechanics transition state calculations. [1] Eksterowicz, J. E.; Houk, K. N. Transition-state modeling with empirical force fields. Chem. Rev. 1993, 93, 2439-2461. [2] Sherrod, M. J.; Menger, F. M. "Transition-state modeling" does not always model transition states. J. Am. Chem. Soc. 1989, 111, 2611-2613. [3] Menger, F. M.; Sherrod, M. J. Origin of high predictive capabilities in transition-state modeling. J. Am. Chem. Soc. 1990, 122, 8071-8075. [4] Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. MacroModel V3.5X. 1990, 11, 440-467. I hope this information is helpful. Ciao, ------------------------------------------------------------------ | Konrad Koehler | Computational Chemistry Group | | internet: koehler@irbm.it | Department of Medicinal Chemistry | | | IRBM | | telephone: +39-6-910-93606 | Via Pontina Km. 30,600 | | fax: +39-6-910-93225 | 00040 Pomezia (Roma) | | | Italy | ------------------------------------------------------------------ =============================================================================== David White wrotes: Dear Dr. Garcia-Laureiro, Professor Tony Ford of the University of Natal in South Africa and I are just about finished a study of 1,3-dipolar additions between diazomethane and some dipolarophiles. However, we have done the entire study using ab initio. We have completed the transition state optimizations and are in the process of doing the frequency calculations. We would be very interested to know the dipolarophiles you are using in your study for potential comparrison of the ab initio and semiempirical results. Sincerely, David White **************************************************************************** * * * * David White * Man is the best computer we can put * * Beckman Institute * aboard a spacecraft -- and the only * * University of Illinois at Urbana- * one that can be mass produced with * * Champaign * unskilled labour * * (217) 244-8371 (fax) * * * (217) 244-1733 * Werner von Braun * * * * **************************************************************************** =============================================================================== E. Lewars wrotes: I believe a semiemp study of the Diels-Alder reaction of heterodienophiles (HNO, HN=NH, etc will appear in THEOCHEM this year; this is related to the topic you asked about. =============================================================================== Again, thank you very much. ******************************************************************************* Dr. Jose Ignacio Garcia-Laureiro Phone : 34-(9)76-350475 Departamento de Quimica Organica Fax : 34-(9)76-567920 Instituto de Ciencia de Materiales de Aragon e-mail: jig@qorg.unizar.es C.S.I.C.-Universidad de Zaragoza jig@cc.unizar.es 50009 ZARAGOZA (SPAIN) jig@msf.unizar.es ******************************************************************************* "And all this science I don't understand it's just my job five days a week..." ELTON JOHN - Rocket man ******************************************************************************* From av@ocirs4.unizh.ch Mon Apr 18 05:29:26 1994 Received: from ocirs4.unizh.ch for av@ocirs4.unizh.ch by www.ccl.net (8.6.4/930601.1506) id FAA14285; Mon, 18 Apr 1994 05:05:21 -0400 Received: by ocirs4.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA11971; Mon, 18 Apr 1994 10:00:52 +0100 Date: Mon, 18 Apr 1994 10:00:52 +0100 From: av@ocirs4.unizh.ch (Alexander Voityuk) Message-Id: <9404180900.AA11971@ocirs4.unizh.ch> To: chemistry@ccl.net Subject: Zn and Cd in MNDO/d < Does your program also support the elements underneath To: chemistry@ccl.net Subject: Hyperpolarizabilities in MOPAC93 Hi Netters. I'm running MOPAC7 in order to calculate first and second order hyperpolarizabilities. The results, I'm obtaining, seem to indicate that there are some problems. For various molecules such as benzene, naphthalene, and anthracene the values of alpha, beta, and gamma are correct at low perturbation energies. At higher values of omega (1.5, 2.0 eV), alpha, beta, and gamma explode. The larger the conjugated system, the lower the perturbation energy at which the NLO values go berserk. For C70, at omega=0.649 eV, the calculations result in an unphysically high value of alpha and a beta (SHG) markedly different from zero (for C70 beta MUST be equal to zero). I was wondering if somebody has encountered the same type of difficulties and if there is a way out Marianna Fanti Istituto di chimica "G. Ciamician" via Selmi n.2 40126 Bologna Italy Tel. 051-259495 e-mail: marianna@treebeard.ciam.unibo.it ****************************************************** From rpetsche@mrg.PHYS.CWRU.Edu Mon Apr 18 08:29:29 1994 Received: from thor.INS.CWRU.Edu for rpetsche@mrg.PHYS.CWRU.Edu by www.ccl.net (8.6.4/930601.1506) id IAA16099; Mon, 18 Apr 1994 08:20:17 -0400 Received: from mrg.PHYS.CWRU.Edu by thor.INS.CWRU.Edu with SMTP (5.65b+ida+/CWRU-1.9.4) id AA13827; Mon, 18 Apr 94 08:19:36 -0400 (from rpetsche@mrg for chemistry@ccl.net) Received: by mrg.phys.cwru.edu (5.57/Ultrix3.0-C) id AA25231; Mon, 18 Apr 94 08:15:10 -0400 Date: Mon, 18 Apr 94 08:15:10 -0400 From: rpetsche@mrg.PHYS.CWRU.Edu (Rolfe G. Petschek) Message-Id: <9404181215.AA25231@mrg.phys.cwru.edu> To: chemistry@ccl.net, marianna@treebeard.ciam.unibo.it Subject: Re: CCL:Hyperpolarizabilities in MOPAC93 Cc: rpetsche@mrg.PHYS.CWRU.Edu >Subject: CCL:Hyperpolarizabilities in MOPAC93 > >the values of alpha, beta, and gamma are >correct at low perturbation energies. At higher values of omega >(1.5, 2.0 eV), alpha, beta, and gamma explode. The larger the conjugated >system, the lower the perturbation energy at which the NLO values go berserk. > >Marianna Fanti > >Istituto di chimica "G. Ciamician" via Selmi n.2 40126 Bologna Italy Mopac uses coupled time dependent hartree fock equations to calculate frequency dependent (hyper) polarizabilities. The iterative method which is currently implemented for solving these equations will not converge to a correct answer unless the frequency is below the frequency of the lowest lying (symmetry allowed, 1's CI) excited state. Rolfe G. Petschek Petschek@cwru.bitnet Associate Professor of Physics rgp@po.cwru.edu Case Western Reserve University (216)368-4035 Cleveland Oh 44106-7079 From MMADRID@B.PSC.EDU Mon Apr 18 10:29:35 1994 Received: from B.PSC.EDU for MMADRID@B.PSC.EDU by www.ccl.net (8.6.4/930601.1506) id KAA17192; Mon, 18 Apr 1994 10:00:40 -0400 From: Date: Mon, 18 Apr 1994 10:01:49 -0400 (EDT) To: chemistry@ccl.net Message-Id: <940418100149.24c14c61@B.PSC.EDU> Subject: CCL: computational X-ray crystallography workshop offered by PSC COMPUTATIONAL X-RAY CRYSTALLOGRAPHY WORKSHOP Pittsburgh Supercomputing Center July 24-27, 1994 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a computational X-ray crystallography workshop. The objective of this workshop is to introduce participants to the theoretical and computational analysis of X-ray crystallography data of both small molecules and macromolecules. Topics will include: the theoretical basis for the minimal function, simulated annealing, molecular replacement, phasing and density modification. The programs SnB, based on Shake and Bake, and X-PLOR will be extensively discussed. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided during the hands-on sessions, or on their own experimental data. No prior supercomputing experience is necessary. Workshop leaders are: Dr. Axel Brunger, Yale University, Dr. Herbert Hauptman, Medical Foundation of Buffalo, Inc. and Dr. Russ Miller, State University of New York at Buffalo. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for academic participants are supported by this grant. Enrollment is limited to 20. Deadline for applications is: May 24, 1994. PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE COMPUTATIONAL X-RAY CRYSTALLOGRAPHY July 24-27, 1994 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by MAY 24, 1994 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, 412/268-4960, or send electronic mail to blankens@psc.edu (internet) *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From wgalazka@chem.uw.edu.pl Mon Apr 18 11:29:37 1994 Received: from sunic.sunet.se for wgalazka@chem.uw.edu.pl by www.ccl.net (8.6.4/930601.1506) id LAA18362; Mon, 18 Apr 1994 11:07:28 -0400 Received: from chem.uw.edu.pl by sunic.sunet.se (8.6.8/2.03) id RAA01816; Mon, 18 Apr 1994 17:07:21 +0200 Received: from [148.81.21.70] (caesar.chem.uw.edu.pl) by chem.uw.edu.pl (4.1/SMI-4.1) id AA07199; Mon, 18 Apr 94 17:04:51 +0200 Organization: Department of Chemistry, University of Warsaw Address: Pasteura 1, 02-093 Warsaw, Poland. Date: Mon, 18 Apr 94 17:04:04 +0100 From: "Wojciech Galazka" Message-Id: <72601.wgalazka@chem.uw.edu.pl> X-Minuet-Version: Minuet1.0_Beta_14.9 Reply-To: X-Popmail-Charset: English To: Chemistry@ccl.net Subject: CACAO program wanted Dear neeters, I am looking for CACAO program - a tool to analyse molecular orbitals on PC. I though it was available on www.ccl.net, as says README file on /pub/chemistry/software. Unfortumately there's no the program anywhere. :( Does anyone know other sites where CACAO is available ? Thanking for any help Wojciech Galazka ///////////////////////////////////////////////////****************** // Wojciech Galazka // * // Computer Center // Chemistry - yes,* // Chemistry Department, University of Warsaw // Distortions- no * // Pasteura 1, 02-093 Warsaw, Poland // * ///////////////////////////////////////////////////****************** From EDGECOMK@QUCDN.QUEENSU.CA Mon Apr 18 17:29:36 1994 Received: from QUCDN.QueensU.CA for EDGECOMK@QUCDN.QUEENSU.CA by www.ccl.net (8.6.4/930601.1506) id RAA23620; Mon, 18 Apr 1994 17:17:23 -0400 Message-Id: <199404182117.RAA23620@www.ccl.net> Received: from QUCDN.QUEENSU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with BSMTP id 6807; Mon, 18 Apr 94 17:17:20 EDT Received: from QUCDN.QUEENSU.CA (NJE origin EDGECOMK@QUCDN) by QUCDN.QUEENSU.CA (LMail V1.1d/1.7f) with RFC822 id 0934; Mon, 18 Apr 1994 17:17:19 -0400 Date: Mon, 18 Apr 1994 17:13 EDT From: EDGECOMK@QUCDN.QueensU.CA To: chemistry@ccl.net Subject: 2nd Cdn. Comp. Chem. Conf. Please find attached the revised 3rd notice for the C4. Hope to see you there! Take care. Ken Edgecombe Third Announcement (revised April 12, 1994) 2nd Canadian Computational Chemistry Conference Deuxieme Conference Canadienne en Chimie Computationelle Queen's University, Kingston, Ontario, Canada May 21-25, 1994 This is the third announcement of the 2nd CCCC. Bringing together Computational Chemists from academia, government, and industry from around the world, the CCCC consists of invited talks, contributed talks, and poster sessions. The program is divided into four general subject areas: Applications of Computational Chemistry: Biological, Chemical, Materials and Pharmaceutical Electronic Structure Computations: Density Functional Theory and Ab Initio Methods Collision and Dynamics Computations Current and Future Trends Plenary speakers: A. Bandrauk (Sherbrooke) Molecular Multiphoton Transitions: Computational Methods From Perturbative to Nonperturbative Regimes R. Bartlett (Florida) Excited States in Coupled-Cluster Theory: Valence, Rydberg and Core Excitations P. Brumer (Toronto) Phase Incoherent Laser Control of Molecular Photodissociation C. Bunge (U.N.A.M., Mexico) Large-Scale Atomic Configuration Interaction Calculations: Computer Programs and Applications E. Carter (U.C.L.A.) New ab initio Algorithms for Solving the Electronic and Geometric Structure Problems G.H.F. Diercksen (Max Planck Inst.) Intelligent Software: The OpenMol Project D.A. Dixon (Dupont) Density Functional Theory Predictions of Molecular Properties and Applications of Computational Chemistry to Atmospheric Chemistry M. Dupuis (IBM) Advances in Parallel Processing: Prospectives and Results P. Kollman (U.C.S.F.) Molecular Dynamics and Free Energy Perturbation Calculations on Complex Molecular Systems P. Mezey (Saskatchewan) High-Resolution Shape Analysis of Macromolecules G. Patey (U.B.C.) Ion Solvation Dynamics R. Poirier (M.U.N.) OSIPE: A Tool for Scientific Programming in FORTRAN D. Salahub (Montreal) Using Density Functional Theory and Other Tools to Model Complex Systems and Processes P. Saxe (Biosym) Force Fields and Massively Parallel Computers G. Scuseria (Rice) Density Functional and Hartree-Fock Theories Applied to Large Systems: The Mechanisms of Fullerene Annealing, Fragmentation and Window Opening J. Tirado-Rives (Yale) MD Simulations of Protein Dynamics and Unfolding R. Wyatt (Texas) Quantum Dynamical Studies of Energy Transfer in Molecules W. Yang (Duke) A Divide-and-Conquer Method and Its Applications to Large Molecules M. Zerner (Florida) Solvent Effects in Quantum Chemistry: Estimating the Effects of Dispersion on Electronic Spectra T. Ziegler (Calgary) Density Functional Theory as a Practical Tool in Studies of Molecular Energetics and Dynamics As well, there will be hardware and software vendor exhibits. Confirmed corporate participants (to date) Canadian Airlines IBM Chapman & Hall Molecular Simulations Cray Research Silicon Graphics DEC Sun Microsystems High Performance Computing Travel: Kingston is accessible directly by bus and train from Montreal, Ottawa, and Toronto and by plane directly from Montreal and Toronto. Canadian Airlines International and their regional partners have been selected as "Official" Airlines for our conference. A 15% discount off the full economy fare will be given when you travel within North America with Canadian to our conference. Also, advance purchase may offer even greater savings. Contact Canadian Airlines' Conventionair office toll-free at 1-800-665-5554 advising them you will be attending the CCCC, on May 21, 1994 in Kingston. Be sure to give our file registration number which is 5503. If booking through a local travel agent make sure they register your booking with the Canadian Airlines' Conventionair Office. Also, members of Canadian Plus will receive 1,000 CP Plus Bonus points for this event along with their mileage points. International delegates (non-North American) may also make use of the Canadian Airlines International Sales Office and coordinate with Canadian Airlines' Conventionair Services. Contact the conference organizers for the applicable international phone numbers. On site registration begins at 2:00PM Sat. May 21, 1994. Scientific sessions end at noon on Wed. May 25, with lunch to follow. Registration: To encourage participation in the conference by undergraduate and graduate students, lower conference fees for these students have been set: Regular Student Plan A: $380.00 (CDN) $330.00 (CDN) Includes accommodation (4 nights), 4 breakfasts, 4 lunches, coffee breaks, and wine and cheese socials. The accommodation consists of a single room in the university residence. Regular Student Plan B: $220.00 (CDN) $190.00 (CDN) Includes 4 lunches, coffee breaks, and wine and cheese socials. Alternate accommodation and restaurants are within walking distance of the conference site. A list of alternate accommodation is available for Plan B registrants. Due to numerous inquiries, spousal and group accomodation rates have been arranged. Contact Ken Edgecombe (see below) for details. Registration fees include appropriate taxes such as the federal Goods and Services Tax (GST). GST Registration Number 107 868 705. To register, send cheque or money order payable to 2nd Canadian Computational Chemistry Conference along with registration information to: Dr. Ken Edgecombe Dept. of Chemistry cccc94@qucdn.queensu.ca Queen's University Kingston, Ontario FAX (613) 545-6669 Canada K7L 3N6 Organizing Committee for the 2nd CCCC: A. D. Becke, K. E. Edgecombe, V. H. Smith, Jr., D. M. Wardlaw, D. F. Weaver, Department of Chemistry, Queen's University Registration Form: -------------------------------------- Name: .............................................................. Address: ........................................................... ........................................................... ........................................................... e-mail: ............................................................ Phone: ........................ FAX: .............................. Status: __ regular __ student __ contributed poster __ attend only __ payment enclosed __ payment sent separately Registration Selection: Plan A:__ Plan B:__ Subject area: ...................................................... Title: ............................................................. ............................................................. ............................................................. Please note that the abstract deadline for inclusion in the book of abstracts has passed. Unless production delays cause a revision of our schedule, abstracts received after today will be distributed loose at the conference. Abstracts should be submitted in camera ready form and limited to one page. If submitted by e-mail please use standard ASCII characters only.  From marg@chem1.chem.swin.oz.au Mon Apr 18 18:29:32 1994 Received: from stan.xx.swin.OZ.AU for marg@chem1.chem.swin.oz.au by www.ccl.net (8.6.4/930601.1506) id SAA24037; Mon, 18 Apr 1994 18:22:48 -0400 Received: from chem1.chem.swin.oz.au ([136.186.11.1]) by stan.xx.swin.OZ.AU (5.59/1.34) id AA08771; Tue, 19 Apr 94 08:19:59 EST Received: by chem1.chem.swin.oz.au (920330.SGI/920502.SGI) for @stan.xx.swin.oz.au:CHEMISTRY@ccl.net id AA27929; Tue, 19 Apr 94 08:18:06 +1000 Date: Tue, 19 Apr 94 08:18:06 +1000 From: marg@chem1.chem.swin.oz.au (Margaret Wong) Message-Id: <9404182218.AA27929@chem1.chem.swin.oz.au> To: CHEMISTRY@ccl.net Subject: helix dipole Dear Networkers Is there any way to calculate the dipole on a helix in a protein. Several papers I have read recently talk about the importance of the helix-dipole but none quantify this value. THANKS Margaret Wong _ Dr Margaret Wong V marg@chem1.chem.swin.oz.au _--_|\ (_)o Chemistry Dept | | mgw@stan.xx.swin.oz.au / \ /\ \ Swinburne Uni /___\ Ph. 03 819 8542 \_.--.x/ Hawthorn,OZ,3122 /_____\ Fax 03 819 0834 v From bwolfe@starman.convex.com Mon Apr 18 19:29:33 1994 Received: from convex.convex.com for bwolfe@starman.convex.com by www.ccl.net (8.6.4/930601.1506) id TAA24336; Mon, 18 Apr 1994 19:13:31 -0400 Received: from starman.convex.com by convex.convex.com (5.64/1.35) id AA10796; Mon, 18 Apr 94 18:10:37 -0500 Received: by starman.convex.com (5.64/1.28) id AA00307; Mon, 18 Apr 94 18:10:34 -0500 Date: Mon, 18 Apr 94 18:10:34 -0500 From: bwolfe@starman.convex.com (Bruce Wolfe) Message-Id: <9404182310.AA00307@starman.convex.com> To: Chemistry@ccl.net, KUS%SUEARN2.BITNET@mps.ohio-state.edu Subject: Re: CCL:CONVEX for ab initio calculations Cc: smigel@starman.convex.com Mikhail Kuzminsky writes: | > Dear Netters ! > CONVEX computers are wide used for computational chemistry. > May somebody estimate the reliability of CONVEX C120 or CONVEX C3xxx > for a case of large e scale non-empirical calculations (for example,G92 > 24h per day :-) ) : > > - how many years will succesfully work magnetic disks > - how long is mean time between computer failures > etc. > > Mikhail Kuzminsky, > Institute of Organic Chemistry Russian Ac. of Sci., > Moscow > KUS@SUEARN2.BITNET A Convex C120 has a MTBF of 15294 hours. A Convex C3210 has a MTBF of 6024 hours. A Convex C3240 has a MTBF of 2457 hours. A Convex C3410 has a MTBF of 2987 hours. A Convex C3440 has a MTBF of 1563 hours. A Convex C3820 has a MTBF of 1204 hours. (We don't have enough C3810's to quote numbers) A Convex C3880 has a MTBF of 1035 hours. That includes all peripherals except terminals. It's configuration is an aggregate configuration based on all US installations. Removal of an item constitutes a failure even if it is not verified as bad upon retest. We have many disks with over ten years operation on them. I would expect between 8-15 years to be a good useful life. Technology seems to determine when disks need to be replaced more than wearout does. MTBF for our disks is generally in the 200,000 to 300,000 hour range. RAID can improve that if needed or if the data is extremely critical. If you are interested, I can have a salesperson call you. A detailed MTBF can be provided for a specific configuration. ___ (o o) =======================---ooO-(_)-Ooo---===================================== Bruce Wolfe Convex Computer Corporation Reliability Manager 3000 Waterview Pkwy (214) 497-4722 Mail Station QAE bwolfe@convex.com Richardson, TX 75080 ============================================================================= From BAELL@mel.dah.csiro.au Mon Apr 18 19:36:46 1994 Received: from dahsun.mel.dah.csiro.au for BAELL@mel.dah.csiro.au by www.ccl.net (8.6.4/930601.1506) id SAA24121; Mon, 18 Apr 1994 18:30:18 -0400 Received: from mhs.mel.dah.CSIRO.AU by dahsun.mel.dah.csiro.au with SMTP id AA27867 (5.67a/IDA-1.5 for <@dahsun.mel.dah.csiro.au:chemistry@ccl.net>); Tue, 19 Apr 1994 08:29:51 +1000 Message-Id: <199404182229.AA27867@dahsun.mel.dah.csiro.au> From: BAELL@mel.dah.csiro.au (Jonathan Baell) To: chemistry@ccl.net (SSchafer) Subject: AM1 conf.analysis Date: Tue, 19 Apr 94 08:28 Dear Steven, A year or so ago I wanted to do a similar thing and my impressions are as follows. I would suggest to use the later versions of AM1 which include parameters for sulfur and phosphorous. AM1 in general would seem to have fewer faults than MNDO - and is more "tried and tested" than PM3 - in predicting correct geometries in conjugated systems and in estimating hydrogen bonding interactions and tautomerism (see Fabian, J. Comp. Chem. 12, 17-35 (1991)), although it's worth knowing some of its limitations with respect to underestimation of rotational barriers (see Fabian, J. Comp. Chem. 9, 369-377 (1988)). For ease and accuracy in conformational studies of non-conjugated (and not too unusual) fragments I would use MM2 or MM3 (see Gundertofte et al, J. Comp. Chem. 12, 200-208 (1991). Remember to consider the effects of solvent and dielectric constant to reflect the environment which your biological results represent. This is relevant even if the bioassay has significant "in vivo" character as you can factor out the effect that molecular hydrophobicity has on transport to the active site (as no doubt you are aware). In vacuuo semiempirical calculations can lead to significant problems when extending the results to a system in, for example, water, and it used not to be a trivial matter to incorporate these effects into such calculations (see Karelson et al, J. Org. Chem. 54, 6030-6034 (1989)) without explicit inclusion of water molecules. However, AMSOL, with which I am unfamiliar, may be the "solution" for these cases. While AM1 outcompetes MNDO with respect to most geometrical calculations, it is MNDO ESP charges that most closely match 6-31G*-derived point charges (see Besler et al, J. Comp. Chem. 11, 431-439 (1990) and Merz Jr., J. Comp. Chem. 13, 749-767 (1992)). Thus if you're not happy with the assumption that molecular mechanics calculations at a constant dielectric of 1 and without electrostatics can be used to reasonably reflect the behaviour of the corresponding charged system in water (or the active site), you might want to look at varying the dielectric constant using the MNDO-ESP (scaled) charges. Whether you set the dielectric to 78 (water) or 4 (a value I've seen recommended for a ligand-protein interface), or a value somewhere in between, or whether you vary the dielectric with distance, I do not know which is best..... ......... .........and would be interested in any information from anyone on what is regarded as the most recommended approach with respect to the consideration of dielectric in ligand-protein interactions, where the protein may or mayn't be membrane-bound: is it a "highly individual" treatment, depending greatly on the microenvironment (active site) more than the macroenvironment (membrane or water)? I would have thought so. Indeed, while on this point, I would have thought that the dielectric of the active site of proteins in membranes would tend to be relatively greater than that which occurs in proteins in an aqueous environment, because in this way nature wins out: in a non-polar macroenvironment a polar "microinteraction" (sorry about all this jargon) would be energetically favourable but in an aqueous macroenvironment a non-polar, hydrophobic active site would be required to produce a significant and far-reaching favourable interaction (for a hydrophobic ligand). Does anyone know of a good discussion paper on active site dielectrics vs protein type? Jonathan Baell From AHOLDER@VAX1.UMKC.EDU Mon Apr 18 20:29:34 1994 Received: from VAX1.UMKC.EDU for AHOLDER@VAX1.UMKC.EDU by www.ccl.net (8.6.4/930601.1506) id UAA24566; Mon, 18 Apr 1994 20:12:40 -0400 From: Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01HBBXIOSRFO9S3U9X@VAX1.UMKC.EDU>; Mon, 18 Apr 1994 19:04:06 CST Date: Mon, 18 Apr 1994 19:04:04 -0600 (CST) Subject: Semiempirical parameterization yet again... To: CHEMISTRY@ccl.net Message-id: <01HBBXIOSRFQ9S3U9X@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Netters, What a firestorm a few innocent comments in answer to a relatively simple question started up! I'd like to very carefully (flame-proof clothing, I hope) take an opportunity to answer some of the issues raised by some of the people in a few previous postings last week in answer to my discussion of AM1 vs. PM3. (An item I posted in reply to a direct question, I might add.) First, what seem to be the issues? I have identified a few from the postings by Joe Leonard (JL) of Wavefunction, Craig Burkhart (CB) at Goodyear, John McKelvey at Kodak (JM), and Chris Cramer (CC) at the University of Minnesota. (I don't want to put words in anyone's mouth, but below seems to an accurate rendering to me. I have also "shaded" them perhaps with questions I have been asked and comments I have heard in the course of my travels and correspondence, so there may be some inferences here they didn't intend.) 1. The parameterization of semiempirical methods is a relatively simple "number-twiddling" task that is only limited by the speed of the computers at hand. (JL and lots of other people) 2. Larger molecules should be used in the molecular basis sets for parameterization (we call this the MBSP). (JL, CB) 3. More molecules and problem systems should be included in the MBSP for better results. (JL, CB) 4. Better experimental data is now available to parameterize against and should be used. (JL, CB) 5. Re-parameterization could give better results within the present semiempirical models of AM1 and PM3. (JL) 6. Property-specific semiempirical methods should perhaps be developed to compute only what we are interested in and to allow us to forget the rest. (JL, CB, CC) 7. Perhaps a new model is needed. (CC) 8. Effort at semiempirical development is being duplicated. (CC, JM) ("The snake oil salesman mounted the soapbox to confront the angry crowd. He began to speak:") I'd like to try to answer these more or less one at a time, but first a few general comments, which I clearly identify as MY SCIENTIFIC OPINION. As such, I would ask that it be respected just as you would anyone else's opinion. This includes not calling me nasty names or accusing me of evil intentions. The development of a semiempirical quantum mechanical model is indeed similar to the development of a molecular mechanics force field in that the objective is to reproduce experimental data. That is about where the similarity ends. The underlying guts of the models are totally different! I can safely say that MM has nothing to do with chemistry, but is more or less a fit to a convenient set of functions. It does have chemical validity in that it gives us good answers to some questions. QM is an entirely different situation, in that the actual arbiters of chemistry, the electrons, are treated directly by mathematical functions. The chemistry come OUT of a model that describes the electrons. This may seem to be a matter of degree to some, but I think that it is an important distinction, especially as it finally applies to parameterization of quantum chemical models. Now, to answer the numbered items above. (1), (2), (3) The speed of computers has indeed greatly enhanced the efficiency of parameterization. Rather than develop "Several/many sets of params" quickly, my group has elected use this power to do parameter- izations more carefully than ever before possible. This involves including larger systems and more molecules in the MBSP, a concept with which I heartily agree! There are some things that will never be modeled properly unless we include them in the MBSP as larger molecules. One of these gentlemen, John McKelvey pointed this out to me quite directly when referring to the poor reproduction of the twist angle in the diphenyl system with AM1. We have also taken more care at examining the structure and complexity of the parameter hypersurface than ever before. This hypersurface is an incredibly complex multidimensional mathematical construct. One must examine it very carefully to find good starting points for further refinement. This concept is directly analogous to the multiple-minima problem for conformer searches. This discussion is also somewhat applicable to item (5). (4) Agreed, more and better experimental data is available now. We are trying to make use of this as much as possible. It should be noted that this is only a marginal improvement over what went before rather than a quantum enhancement. (5), (7) PM3 was essentially a re-parameterization of AM1 using a more mathematical approach (as opposed to chemical intuition and knowledge) to deriving parameters and applying very powerful computers. It was better for some items than AM1, but as my previous posting showed, it was only marginally better. It also possessed some severe problems. Chris is correct: to get better results, we need a new MODEL. The work I am aware of along these lines is underway here in my lab at the University of Missouri-Kansas City (with C. Jie and R. Dennington) and under the direction of Prof. Walter Thiel at the Univ. of Zurich, in collaboration with A. Voityuk. Our work involves SAM1, which is a new model developed primarily under the guidance of Michael Dewar. It is indeed a new model and it uses a new approach to compute the two-electron/two-center repulsion integrals (TERIs) for all systems. This new approach allows us to also treat d-orbitals explicitly. Results have been published for C, H, On, N, F, Cl, Br, and I in our new model and we intend to publish a method paper as soon as the final model for transition metals is finalized and tested. (M. J. S. Dewar, C. Jie, G. Yu, Tetrahedron 23, 5003 (1993); A. J. Holder, R. D. Dennington, C. Jie, Tetrahedron 50, 627 (1994)) Prof. Thiel's work involves MNDO/d, which uses a new version of the multipole expansion method to circumvent the TERI problem with d-orbitals. MNDO/d is an addition to the MNDO model developed by Prof. Thiel in collab- oration with Prof. Dewar in 1977. (W. Thiel, A. A. Voityuk, Theoretica Chimica Acta 81, 391 (1992); W. Thiel, A. A. Voityuk, International Journal of Quantum Chemistry 44, 807 (1993)) (8) As shown above, at least for the cases of Prof. Thiel's work and that work being done in my lab, effort is NOT being duplicated. These are two clearly different approaches to the same problem, and I suspect that both will find users and adherents. (6) I have left the property-specific semiempirical method question for last. This one is also perhaps the one most prone to debate and opinion. Personally, I disagree with this entire concept. Chris Cramer makes the point that one of the strengths of ab initio methods is their generality. I would like to make this same case for the more popular semiempirical methods such as SINDO1, MINDO3, MNDO, AM1, PM3, SAM1, and MNDO/d. Contrast these to INDO/S which is acknowledged to really work only for spectra. (Yes, I know that papers have shown it works for other things sometimes, but even the authors of the method think of that as a fortuitous circumstance.) Dewar's methods have found such wide approval, application, and acceptance simply because they are GENERAL. If we paramet- erize semiempirical methods for heats for formation only or for a single class of compounds only, we may gain in accuracy, but we lose in the capa- bility to have a single approach to many problems. Now, back to what I was saying about models above. (Bet you thought I wasn't going to get back to that, huh?) Semiempirical models are chemical models based on a somewhat direct relationship to nature. In my way of thinking, stretching this model away from all correspondence with some physical quantities (which are actually supposed to be IN THE MODEL) to gain an additional modicum of accuracy for the property YOU consider critical is not model development, it is "number-twiddling" of the highest order! Semiempirical parameters must fit into chemistry. This is why we include dipole moments in the parameterization of a method that some people use to only compute heats of formation. If the method cannot do some sort of systematic treatment of dipole moments and is based on the same quantum mechanical approach that brings us the heats of formation, how can we trust it? Finally, (bet you thought I'd never quit) where are the calls for special ab initio basis sets to compute reaction energetics? What about special basis sets for fluoroethers? Remember, basis sets are "parameterized" just like semiempirical methods. (Where do you think those exponents come from?) We don't ask for these because they would destroy the generality of the approach. While some may choose the track of specialized semiempirical methods, we will proceed with developing general approaches. ("The snake oil salesman descends from the soapbox to thunderous applause.") Andy Holder 4/18/94 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || Internet Addr: aholder@vax1.umkc.edu Univ. of Missouri - Kansas City || Phone Number: (816) 235-2293 Spencer Chemistry, Room 315 || FAX Number: (816) 235-5502 Kansas City, Missouri 64110 || =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=