From dave@carbon.chem.csiro.au Wed Jun 23 10:25:31 1993 Message-Id: <199306230523.AA22210@shark.mel.dit.csiro.au> Date: Wed, 23 Jun 93 15:25:31 EST From: (Dr.) Dave Winkler Subject: Computational Chemistry Symposium at 5ACC To: R.Nobes@anu.edu.au, yatesb@postoffice.utas.edu.au, CHMIGORN@NUSVM.bitnet, CALL FOR PAPERS 5TH ASIAN CHEMICAL CONGRESS (8-11 NOVEMBER) is sponsoring a symposium "PERSPECTIVES IN APPLIED COMPUTATIONAL CHEMISTRY" MING COURT HOTEL, KUALA LUMPUR NOVEMBER 11, 1993 The Symposium will emphasize all aspects in applications of computational chemistry, including small molecules, polymer systems, biological systems, and materials, surfaces, interfaces, and clusters. The Program will include three plenary lectures and several invited speakers as well as contributed oral and poster sessions. For registration and abstract submission details contact: Executive Secretary Institiut Kimia Malaysia 129B Jalan Aminuddin Baki Taman Tun Dr Ismail 60000 Kuala Lumpur Phone/fax: 60-3-718-9909 Further information on the computational chemistry symposium can be obtained from: Dr. Dave Winkler CSIRO Division of Chemicals and Polymers Private Bag 10, Clayton 3168, Australia Phone: 61-3-542-2244 Fax: 61-3-543-8160 Email: dave@carbon.chem.csiro.auI have The symposium will comprise four sessions: Chemical Applications of Computational Chemistry ------------------------------------------------ Plenary Speaker: Prof. Leo Radom (Australian National University, Canberra) "Chemistry by Computer: A Theoretical Approach to Structure and Mechanism" Biological Applications of Computational Chemistry -------------------------------------------------- Plenary Speaker: Dr. Gerry Maggiora (Upjohn Laboratories, Kalamazoo) "Current and Future Applications of Computational Chemistry in the Biosciences" Materials Applications of Computational Chemistry ------------------------------------------------- Plenary Speaker: Prof. Erich Wimmer (Biosym Technologies, Paris) " An Overview of the Materials Applications of Computational Chemistry and Perspectives" Mixer, Workshop, Trade Display and Poster Session. -------------------------------------------------- Poster session and displays of Silicon Graphics workstations, Cray's UniChem molecular orbital software, Biosym Technology's molecular modelling software. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PROGRAM FOR ONE DAY MEETING ON COMPUTATIONAL CHEMISTRY ------------------------------------------------------------ KUALA LUMPUR 11TH NOVEMBER 1993 09.00-09.10 WELCOME AND OFFICIAL OPENING (H.H.HUANG) SESSION 1. CHEMICAL APPLICATIONS OF COMPUTATIONAL CHEMISTRY 09.10-09.50 PLENARY 1 L. Radom RChemistry by Computer: A Theoretical Approach to Structure and MechanismS{Cray} 09.50-10.10 Contributed paper 10.10-10.30 Mok Kam Wah R MO calcs on Transition metalsR {Uni HK} 10.30-10.50 MORNING TEA SESSION 2. BIOLOGICAL APPLICATIONS OF COMPUTATIONAL CHEMISTRY 10.50-11.30 PLENARY 2 G. Maggiora RCurrent and Future Applications of Computational Chemistry in the BiosciencesS {Upjohn} 11.30-11.50 Yong Lee RModelling of Aldose Reductase InhibitorsS {NIH} 11.50-12.10 Contributed paper 12.00-13.30 LUNCH AND TRADE DISPLAY SESSION 3. MATERIALS APPLICATIONS OF COMPUTATIONAL CHEMISTRY 13.30-14.10 PLENARY 3 Prof. E. Wimmer RMaterials Applications of Computational Chemistry and PerspectivesS {Biosym} 14.10-14.30 Contributed paper 14.30-14.50 Contributed paper 14.50-15.10 AFTERNOON TEA SESSION 4. MIXER, WORKSHOP, TRADE DISPLAY, POSTER SESSION 15.10-17.30 MIXER, WORKSHOP, TRADE DISPLAY AND POSTER SESSION {Cray Asia/pacific, Biosym Technologies, Silicon Graphics} >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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" From imtvi06@cc.csic.es Wed Jun 23 09:05:14 1993 Date: Wed, 23 Jun 1993 9:05:14 UTC+0100 From: Luis Montero Subject: 32 bit FORTRAN in PC's To: chemistry@ccl.net (confirm) Message-Id: <398*/S=imtvi06/OU=cc/O=csic/PRMD=iris/ADMD=mensatex/C=es/@MHS> Madrid, June 23, 1993 Dear netters:g I ahve some experience with 32 bit FORTRAN compilers in PC's. - WATCOM f77/386 is fast running. However, instructions are not so clear to obtain easily the appropriate executables from large programs that have been compiled in different modules to linked together for any 32 bit Windows and the DOS extender provided in the package. Support is not provided by e-mail, or at least they do not inform their e-mail address easily. I had troubles with a large program which have been previously compiled by 16 bit Microsoft FORTRAN 5.1 and gave wrong calculation results in unchanged routines, for unknown reasons. - LAHEY EM32 FORTRAN is appreciated by colleagues who use it. I have not my own experience. I appreciated very much the simplicity, capacity and fastness of the previous 16 bit version. - NDP 32 bit FORTRAN have been tested by coworkers and they argument a very good performance. I used it sometime and it became hard for large programs because the lack of .OBJ modules in the version I used. I did not go very deep into it. I am waiting for a promised 32 bit FORTRAN compiler from Microsoft. Best regards, Luis Montero Universidad de La Habana and CSIC, Madrid e-mail Madrid: imtvi06@cc.csic.es e-mail Havana: silicon%ceniai.cu@igc.apc.org From mercie@cumc.cornell.edu Wed Jun 23 02:21:30 1993 Date: Wed, 23 Jun 1993 06:21:30 -0400 (EDT) From: Gustavo Mercier Subject: Re: Contracted basis sets To: ALHINAI%EGFRCUVX.BITNET@phem3.acs.ohio-state.edu Message-Id: On Tue, 22 Jun 1993 ALHINAI%EGFRCUVX.BITNET@phem3.acs.ohio-state.edu wrote: > Hi netters , > > Could somebody help me find contracted basis sets for transition metal . > I need them to be : > 1) of double zeta quality . > 2) having their diffuse d functions . > 3) preferebly optimized for the 4s 3d**(n-1) or 3d**(n) configurations > > Here are some references: Review article: E. R. Davidson and D. Feller Chem Rev (1986) 86,681-696 "Basis Set Selection for Molecular Calculations" Minimal Basis sets (but track the reference to more extended ones) H. Tatewaki and S. Huzinaga (1979) J Chem Phys 71,4339-4348 H. Tatewaki, Y. Sakai, and S. Huzinaga (1981) J. Comp. Chem. 2,278-286 Supplemental functions S. P. Walch, C. W. Bauschlicher, Jr., and C. J. Nelin J. Chem. Phys. (1983) 79,3600-3602 Effective Core Potentials (for Gaussian type computations HF,CI,MP2...) P.J. Hay and W. R. Wadt J. Chem. Phys. (1985) 82,270-283 W. R. Wadt and P. J. Hay SAME JOURNAL pages 284-298 P. J. Hay and W. R. Wadt SAME JOURNAL pages 299-310 (for density functional computations) G. B. Bachelet, D. R. Haman and M. Schulter Phys. Rev. B (1982) 26,4199-4228 Hope this will give your a start! Gus Mercier mercie@cumc.cornell.edu From hanv01.dnet.sandoz.com!fox_g@sandoz.com Wed Jun 23 03:08:55 1993 Message-Id: <199306231111.AA04235@tigger.jvnc.net> Date: Wed, 23 Jun 93 07:08:55 -0400 From: fox_g@hanv01.dnet.sandoz.com To: "chemistry@ccl.net"@sndzeh.dnet.sandoz.com Subject: HCN=>HNC PES surface Dear Netters, If anyone has an electronic version of a PES for the isomerization of HCN => HNC could you please forward it to me. The surface could be either analytical or a discrete set of points in any coordinate system at any level of theory. Thanks, Gary Fox fox_g@hanv01.dnet.sandoz.com (201) 503-7735 off. (201) 503-6357 Fax From jwest@ndb.rutgers.edu Wed Jun 23 03:14:46 1993 Date: Wed, 23 Jun 93 07:14:46 -0400 From: jwest@ndb.rutgers.edu (John Westbrook) Message-Id: <9306231114.AA02701@ndb.rutgers.edu> To: chemistry@ccl.net Subject: Gaussian 9x and HP 735/755 Dear netters, I am interested in installing Gaussian 92 on an HP 735 workstation. I understand that there may be some problems with Gaussian on this platform. I would appreciate any information or experiences anyone would be willing to share about Gaussian on the new HP systems. I will happily post a summary of any direct responses. **************************************************************************** * John Westbrook Ph: (908) 932-5156 * * Department of Chemistry Fax: (908) 932-5958 * * Rutgers University * * PO Box 939 e-mail: jwest@ndb.rutgers.edu * * Piscataway, NJ 08855-0939 * **************************************************************************** From jabs@chemie.uni-halle.d400.de Wed Jun 23 17:14:01 1993 Date: Wed, 23 Jun 1993 15:14:01 +0200 From: jabs@chemie.uni-halle.d400.de Message-Id: <930623151400*/S=jabs/OU=chemie/PRMD=UNI-HALLE/ADMD=DBP/C=DE/@MHS> To: chemistry@ccl.net Subject: CSD search Hi, has anybody experiences in search of hydrogen bonds (R-O-H..OHR, intra and intermolecular) in the Cambridge Database with output of O..H-distances and the O-H..O- angle? Thanks in advance, Andreas From MODEL1@kchk.ch-pwr.wroc.edu.pl Wed Jun 23 10:24:41 1993 To: chemistry@ccl.net From: MODEL1@kchk.ch-pwr.wroc.edu.pl Organization: Inst. of Phys. and Theor. Chem. TUW Date: 23 Jun 93 16:01:28 MET Subject: MOLECULE COORDINATES FITTING Message-Id: I'm looking for a source text of a program (Pascal, Turbo Pascal, C) which can fit coordinates of one molecule to another. I am not a member of "CHEMISTRY"- group and so please send the reply using my individual adress: MODEL1@KCHK.CH-PWr.WROC.EDU.PL From youngdc@cemvax.cem.msu.edu Wed Jun 23 06:16:04 1993 Message-Id: <199306231420.AA18801@oscsunb.ccl.net> Date: Wed, 23 Jun 1993 10:16:04 -0400 From: youngdc@cemvax.cem.msu.edu To: CHEMISTRY@ccl.net Subject: Transition metal basis sets In regards to the request for a contracted transition metal basis sets, an often used one is presented in the paper "Gaussian basis sets for molecular calculations. The representation of 3d orbitals in trasition-metal atoms" P. Jeffrey Hay, J. Chem. Phys., 66, 4377, (1977) As far as contraction schemes for Wachter's basis set, it is probably easiest to look up some of the theoretical work done by Harrison or Bauschlicher or Roos or Gordon, to name a few. Good luck, YOUNGDC@CEMVAX.CEM.MSU.EDU From lief@zeno.rice.edu Wed Jun 23 06:13:16 1993 From: Eugene Lief Message-Id: <9306231613.AA11033@zeno.rice.edu> Subject: Finite element method in atomic physics. To: CHEMISTRY@ccl.net, DEAL@kzoo.edu Date: Wed, 23 Jun 93 11:13:16 CDT Dear Netters: For those of you who are interested in finite element method in calculation of the charge density I am writing some tips from my experience. Interested parties are encouraged to ask more specific questions. First, it turned out that the finite element method has its main advantage in cases of complicated geometry. You can specify elements of various forms and sizes which is important, for instance, if you calculate tensions in a bridge of irregular form and you want to have finer grid in some critical places. In my experience, a square mesh could be easier dealt with using a finite DIFFERENCE method, which is basically replacement of derivatives of all orders by finite differences. If all cells are identical, this is trivial, as well as the boundary conditions. I solved a non-standard non-linear equation describing atomic charge density in a strong magnetic field. I had a peculiar normalization condition there, and it was much easier to deal with it in the framework of a finite DIFFERENCE method. I had to deform the domain to satisfy it. I would be happy to provide more detailed description if somebody is interested. Regards, Gene. P.S. The paper has just been submitted to Phys. Rev. A. The preprint is available upon request. : Eugene Lief : Phone (713)527-8750, ext. 3514, 2651. : : Rice University, Department of : E-mail LIEF@SPACSUN.RICE.EDU, : : Space Physics and Astronomy, : LIEF@ZENO.RICE.EDU . : : 6100 S.Main st., Houston, TX : Telex 556457, FAX (713) 285-5143. : : 77251-1892. : : From schw0531@compszrz.zrz.tu-berlin.de Wed Jun 23 20:59:10 1993 Date: Wed, 23 Jun 93 18:59:10 +0200 From: Prof. Dr. Helmut Schwarz Message-Id: <9306231659.AA26638@compszrz.zrz.tu-berlin.de> To: CHEMISTRY@ccl.net Subject: iodine Hi netters, I am interested on some relativistic calculations on iodine dimer in order to compare the pseudopotential results. I there somebody working on this topic? Also all electron calculations would be interresting. Thanks Jan Hrusak schw0531@compszrz.zrz.tu-berlin.de From yama@molbio.ethz.ch Wed Jun 23 21:39:03 1993 From: Bernhard Anton Pabsch Date: Wed, 23 Jun 93 19:39:03 +0200 Message-Id: <9306231739.AA21573@noldi> To: CHEMISTRY@ccl.net Subject: genetic algorithms for conformational search High Netters, just heard a talk given by PV Conveney (Cambridge) on Order, Chaos & Creativity: from chemical self organization to artificial life pointing out that one can solve hard optimization problems with the help of genetic algorithms in the manner, that the best solution will be generated and then filtered out by a process of simulated evolution. Has anybody heard or applied such approach to conformational search? thanks for listening science is art bap-man ----------------------------------------------------------------------------- Bernhard A. Pabsch yama@molbio.ethz.ch Laboratorium fuer organische Chemie MOM_10@CZHETH5A.bitnet ETH Hoenggerberg (HPM G32) Tel. ++41 1 377 34 89 CH-8093 Zuerich/Switzerland Fax ++41 1 372 00 53 ----------------------------------------------------------------------------- From cramer@staff.tc.umn.edu Wed Jun 23 10:51:52 1993 Message-Id: <0012c28c269005900@staff.tc.umn.edu> From: "Christopher J Cramer-1" Subject: Nonprofit software announcement To: chemistry@ccl.net Date: Wed, 23 Jun 93 15:51:52 CDT New Version Announcement AMSOL-version 3.5 A new version (3.5) of AMSOL is now available. This will be cataloged by QCPE as program 606-version 3.5. AMSOL is a program for calculating the free energy of solvation by semiempirical molecular orbital theory using any of the following models: AM1-SM1, AM1-SM1a, AM1-SM2, or PM3-SM3. A subset of AMSOL is a very portable version of AMPAC (based on version 2.1, by D. A. Liotard, E. F. Healy, J. M. Ruiz, and M. J. S. Dewar), which has been run successfully on a wide variety of Unix platforms, including Cray supercomputers running UNICOS and Unix workstations manufactured by DEC, IBM, Silicon Graphics, and Sun. The newest addition to this list is DEC, represented by the 3000/500 AXP, running the OSF/1 version of Unix. AMSOL version 3.5 is based on version 3.0.3. Version 3.0.3 has 2 bug fixes compared to version 3.0.2 (which has been distributed by QCPE since late April, 1993) and has 25 bug fixes and minor enhancements as compared to version 3.0.1 (which is the most recent version to have been _announced_ by QCPE). The further enhancements included in version 3.5 are entirely concerned with speeding up the solvation calculations: 1. A new algorithm, called GEPOL, for evenly distributing points on the surface of the spheres used in calculating the surface areas has been added as an option to the code. The enhancement is based on version 12.0 of GEPOL by E. Silla, I. Tunon, and J. L. Pascual-Ahuir. The algorithm places a generic pentakisdodecahedron on each sphere to divide it into triangular tesserae that guarantee a symmetrical distribution of points on the surface. 2. The method for calculating the surface areas has been modified to increase performance. These improvements have be accomplished primarily by saving more information, using the cosine law (as suggested by R. Le Goas, see the article by Le Goas in forthcoming issue of QCPE Bulletin), and eliminating half spheres of uninvolved surface points >from the area calculations based on simple checks described in the on- line manual. Using identical settings to those in AMSOL version 3.0.3, version 3.5 obtains the same results but experiences a geometric mean speedup factor of 4.2 for neutral molecules and 3.2 for ionic species over the applicable portions of the test suite. 3. In AMSOL version 3.5, the flexibility of the code has been enhanced by the addition of keywords that allow the user to control the number of points distributed on each sphere's surface when calculating the solvent-accessible surface area. This allows the user, with the aide of a table provided in the manual, to obtain the desired compromise of numerical precision and speed for a given application. The default numerical parameters in version 3.5 yield the same average precision (~0.05 kcal) as in versions 3.0 - 3.0.3 with the speedups mentioned above, but by decreasing the precision to 0.4 kcal the speed of the calculation can be increased by an additional factor of 4. This can be very useful for preliminary exploratory studies on large molecules. The authors of version 3.5 are Christopher J. Cramer, Gillian C. Lynch, Gregory D. Hawkins, and Donald G. Truhlar of the University of Minnesota. In addition to making the enhanced capabilities of version 3.5 available at this time, the authors want it known that even more efficient versions, to be called versions 4.0 and 4.1, are now in preparation in collaboration with Daniel Liotard of the University of Bordeaux. We anticipate release within the next six to twelve months. We make this point so that interested parties may make an informed decision if the QCPE medium cost is a concern. AMSOL version 3.5 is copyrighted but not licensed. There is no user fee, and QCPE distributes it for the usual handling charge. The version 3.5 distribution automatically includes version 3.5c, which incorporates extra speedups on Cray supercomputers. The distribution includes an "on-line manual" for AMSOL, which is an ASCII documentation file. QCPE also distribution a copy of the (required) ampac manual with each order for AMSOL. -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 From AHOLDER@VAX1.UMKC.EDU Wed Jun 23 12:44:29 1993 Date: Wed, 23 Jun 1993 17:44:29 -0500 (CDT) From: Andy Holder Subject: SAM1 reference To: CHEMISTRY@ccl.net Message-Id: <01GZQ5C7NOF6AOKQF6@VAX1.UMKC.EDU> Hi netters. For those of you interested, Michael Dewar's new SAM1 method now has an official reference. It is as follows: Dewar, M. J. S.; Jie, C.; Yu, G. Tet. 1993, 23, 5003. This is primarily a listing of results for the new method for a vast array of systems. It also compares quite favorably with AM1 and PM3. A more complete paper describing the model will be forthcoming >from my lab in the next year. Professor Dewar felt it important to move ahead on these elements (treated without d-orbitals) because of the superior quality of results for C, H, O, N, F, Cl, Br, and I. We have completed work on Si and S and are beginning work on P, Fe, and Cu. Thanks, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 315 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From youngdc@cemvax.cem.msu.edu Wed Jun 23 18:35:46 1993 Message-Id: <199306240240.AA29379@oscsunb.ccl.net> Date: Wed, 23 Jun 1993 22:35:46 -0400 From: youngdc@cemvax.cem.msu.edu To: CHEMISTRY@ccl.net Subject: finite element methods, etc In response to the recent request for information about application of the finite element method to quantum mechanics, here is one reference "On the Numerical Solution of the Multidimensional Vibrational Time-Independent Schroedinger Equation" J.R. Alvarez-Collado, R.J. Buenker, J. Comp. Chem., 13, 2, 135-141 (1992) They look at the finite element method and finite difference method (both standard partial differential equation numerical solution techniques). They also present their own modification of the finite element method and apply all of the above to vibrational mode determination. The general gist of these techniques seems to be that they still require a large amount of computational power to get much accuracy. (perhaps on the order of CISD or more). However, it is still a very worthwhile thing to try using some of these methods, since they may shed light on weaknesses of variational and perturbational methods as well as providing insight into such things as correlation. If anyone knows of any similar studies, particularily about correlation, I would like to see your comments or a summary posted on this list. YOUNGDC@CEMVAX.CEM.MSU.EDU