From shokhen@post.tau.ac.il Tue Jun 17 05:49:35 1997 Received: from post.tau.ac.il for shokhen@post.tau.ac.il by www.ccl.net (8.8.3/950822.1) id FAA16366; Tue, 17 Jun 1997 05:16:52 -0400 (EDT) Received: from etgar.tau.ac.il (etgar.tau.ac.il [132.66.16.7]) by post.tau.ac.il (8.8.5/8.8.4) with ESMTP id MAA27674 for ; Tue, 17 Jun 1997 12:12:34 +0300 (IDT) Received: from localhost (shokhen@localhost) by etgar.tau.ac.il (8.8.5/8.7.3) with SMTP id MAA09005 for ; Tue, 17 Jun 1997 12:16:44 +0300 (IDT) X-Authentication-Warning: etgar.tau.ac.il: shokhen owned process doing -bs Date: Tue, 17 Jun 1997 12:16:44 +0300 (IDT) From: shochen michael To: chemistry@www.ccl.net Subject: Virial theorem: -V/T=10.2 in Gaussian 94 ! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear users of the Gaussian 94, Gaussian 94, Revision D.1 is in a serious conflict with the Virial theorem ( -V/T = 2 ): the calculated values are 10.1875 for the RHF/6-31+G* , and 12.8451 for the RHF/D95+(d) What is very funny, that in all of the cases I got a message from Gaussian about the normal termination! These strange results I got for different molecules. I think that something is wrong with the diffusion basis sets (+), because the calculations of the same molecules performed in the RHF/6-31* or B3LYP/6-31* satisfied to the Virial theorem. In addition. In some of my calculations, where RHF/6-31+G* gave the correct results, the B3LYP/6-31+G* failed in the middle of calculation. In contrary, the B3LYP/6-31* gave the correct results with the normal termination. The problem is that I need to calculate anionic systems, so I need to use the basis sets containing the diffusion functions. I'll be very appreciated if somebody give me an advice how to work aroud. Thank you in advance, Michael P.S. Please find enclosed one example, where the Gaussian 94 failed in the Viral theorem, but gave a message about the normal termination. The first is an input file, which is followed by the fragments of the related output file. ******************************************* %Chk=ts3 %Mem=10000000 # RHF/6-31+G* SCF=DIRECT TEST TC ANION 3-21G* OPTIMIZED -1 1 C C,1,R2 C,1,R3,2,A3 C,1,R4,2,A4,3,D4,0 C,2,R5,1,A5,3,D5,0 C,3,R6,1,A6,2,D6,0 C,4,R7,1,A7,2,D7,0 O,4,R8,1,A8,7,D8,0 O,2,R9,1,A9,5,D9,0 O,3,R10,1,A10,6,D10,0 S,4,R11,1,A11,7,D11,0 C,5,R12,2,A12,1,D12,0 Cl,5,R13,2,A13,12,D13,0 Cl,6,R14,3,A14,1,D14,0 H,7,R15,4,A15,1,D15,0 H,7,R16,4,A16,15,D16,0 H,7,R17,4,A17,15,D17,0 H,8,R18,4,A18,1,D18,0 C,11,R19,4,A19,1,D19,0 H,10,R20,3,A20,1,D20,0 H,12,R21,5,A21,2,D21,0 H,19,R22,11,A22,4,D22,0 H,19,R23,11,A23,22,D23,0 H,19,R24,11,A24,22,D24,0 Variables: R2=1.433 R3=1.38673862 R4=1.5390065 R5=1.41828911 R6=1.3844898 R7=1.53794766 R8=1.41649921 R9=1.28195164 R10=1.3775275 R11=1.87361576 R12=1.36318964 R13=1.75653209 R14=1.7541639 R15=1.08280284 R16=1.08309972 R17=1.07916032 R18=1.01268356 R19=1.80866221 R20=0.97133208 R21=1.06989205 R22=1.07949525 R23=1.08005278 R24=1.08174442 A3=120.89289857 A4=118.78207179 A5=115.11617584 A6=120.72497989 A7=110.9080782 A8=113.1871631 A9=123.41661447 A10=122.47355805 A11=111.8749713 A12=123.44545454 A13=117.47214039 A14=120.32194677 A15=109.33924187 A16=107.18210973 A17=111.48826877 A18=108.39740524 A19=97.79784087 A20=111.00502497 A21=120.27528426 A22=106.25519656 A23=111.30530935 A24=108.92560816 D4=-176.2593885 D5=0.98160734 D6=-0.86658381 D7=115.23042257 D8=-121.8826806 D9=179.44676434 D10=-179.28132269 D11=119.13311047 D12=-0.29849994 D13=179.82921589 D14=179.51507708 D15=179.93467218 D16=117.73509895 D17=-122.73099561 D18=6.33840667 D19=66.14258581 D20=-39.70418622 D21=-179.97219346 D22=44.76253312 D23=-119.69422493 D24=118.82376558 ****************************************** Entering Gaussian System, Link 0=g94 Initial command: /ext/g94/l1.exe /tmp/g94-8024.inp -scrdir=/tmp/ Entering Link 1 = /ext/g94/l1.exe PID= 8026. Cite this work as: Gaussian 94, Revision D.1, M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. Keith, G. A. Petersson, J. A. Montgomery, K. Raghavachari, M. A. Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. P. Stewart, M. Head-Gordon, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1995. *************************************** Gaussian 94: SGI-G94RevD.1 1-Feb-1996 26-May-1997 *************************************** %Chk=ts3 %Mem=10000000 ----------------------------- # RHF/6-31+G* SCF=DIRECT TEST ----------------------------- 1/38=1/1; 2/12=2,17=6,18=5/2; 3/5=1,6=6,7=11,11=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,32=1,38=4/2; 6/7=2,8=2,9=2,10=2,19=1,28=1/1; 99/5=1,9=1/99; ------------------------- TC ANION 3-21G* OPTIMIZED ------------------------- Symbolic Z-matrix: Charge =-1 Multiplicity = 1 C C 1 R2 C 1 R3 2 A3 C 1 R4 2 A4 3 D4 0 C 2 R5 1 A5 3 D5 0 C 3 R6 1 A6 2 D6 0 C 4 R7 1 A7 2 D7 0 O 4 R8 1 A8 7 D8 0 O 2 R9 1 A9 5 D9 0 O 3 R10 1 A10 6 D10 0 S 4 R11 1 A11 7 D11 0 C 5 R12 2 A12 1 D12 0 Cl 5 R13 2 A13 12 D13 0 Cl 6 R14 3 A14 1 D14 0 H 7 R15 4 A15 1 D15 0 H 7 R16 4 A16 15 D16 0 H 7 R17 4 A17 15 D17 0 H 8 R18 4 A18 1 D18 0 C 11 R19 4 A19 1 D19 0 H 10 R20 3 A20 1 D20 0 H 12 R21 5 A21 2 D21 0 H 19 R22 11 A22 4 D22 0 H 19 R23 11 A23 22 D23 0 H 19 R24 11 A24 22 D24 0 Variables: R2 1.433 R3 1.38674 R4 1.53901 R5 1.41829 R6 1.38449 R7 1.53795 R8 1.4165 R9 1.28195 R10 1.37753 R11 1.87362 R12 1.36319 R13 1.75653 R14 1.75416 R15 1.0828 R16 1.0831 R17 1.07916 R18 1.01268 R19 1.80866 R20 0.97133 R21 1.06989 R22 1.0795 R23 1.08005 R24 1.08174 A3 120.8929 A4 118.78207 A5 115.11618 A6 120.72498 A7 110.90808 A8 113.18716 A9 123.41661 A10 122.47356 A11 111.87497 A12 123.44545 A13 117.47214 A14 120.32195 A15 109.33924 A16 107.18211 A17 111.48827 A18 108.39741 A19 97.79784 A20 111.00502 A21 120.27528 A22 106.2552 A23 111.30531 A24 108.92561 D4 -176.25939 D5 0.98161 D6 -0.86658 D7 115.23042 D8 -121.88268 D9 179.44676 D10 -179.28132 D11 119.13311 D12 -0.2985 D13 179.82922 D14 179.51508 D15 179.93467 D16 117.7351 D17 -122.731 D18 6.33841 D19 66.14259 D20 -39.70419 D21 -179.97219 D22 44.76253 D23 -119.69422 D24 118.82377 Rotational constants (GHZ): 0.5087519 0.3695608 0.2482086 Isotopes: C-12,C-12,C-12,C-12,C-12,C-12,C-12,O-16,O-16,O-16,S-32,C-12,Cl-35,Cl-3 5,H-1,H-1,H-1,H-1,C-12,H-1,H-1,H-1,H-1,H-1 Standard basis: 6-31+G(d) (6D, 7F) There are 315 symmetry adapted basis functions of A symmetry. Crude estimate of integral set expansion from redundant integrals=1.000. Integral buffers will be 262144 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned on. 315 basis functions 588 primitive gaussians 69 alpha electrons 69 beta electrons nuclear repulsion energy 1398.0344976685 Hartrees. One-electron integrals computed using PRISM. There are 5 eigenvalues of the overlap less than 1.0D-05 The smallest eigenvalue of the overlap matrix is 9.126D-07 Projected CNDO Guess. Warning! Cutoffs for single-point calculations used. Requested convergence on RMS density matrix=1.00D-04 within 64 cycles. Requested convergence on MAX density matrix=1.00D-02. Requested convergence on energy=5.00D-05. Restarting both DIIS and incremental Fock formation. Restarting both DIIS and incremental Fock formation. Convergence on energy, delta-E=3.33D-05 SCF Done: E(RHF) = -17398.0240946 A.U. after 45 cycles Convg = 0.2007D-03 -V/T = 10.1875 S**2 = 0.0000 ********************************************************************** Population analysis using the SCF density. ********************************************************************** Alpha occ. eigenvalues -- ********************-396.43580-185.98863-106.54088 Alpha occ. eigenvalues -- -106.43078 -93.41316 -35.15903 -25.79301 -22.01826 Alpha occ. eigenvalues -- -21.87731 -21.82000 -12.58010 -12.55300 -12.53076 Alpha occ. eigenvalues -- -12.49788 -12.46177 -12.44858 -12.42837 -12.41377 N-N= 1.398034497668D+03 E-N=-7.089851088751D+03 KE= 1.893656502354D+03 Test job not archived. 1\1\GINC-ETGAR\SP\RHF\6-31+G(d)\C9H9Cl2O3S1(1-)\SHOKHEN\26-May-1997\0\ \# RHF/6-31+G* SCF=DIRECT TEST\\TC ANION 3-21G* OPTIMIZED\\-1,1\C\C,1, 1.433\C,1,1.38673862,2,120.89289857\C,1,1.5390065,2,118.78207179,3,-17 6.2593885,0\C,2,1.41828911,1,115.11617584,3,0.98160734,0\C,3,1.3844898 ,1,120.72497989,2,-0.86658381,0\C,4,1.53794766,1,110.9080782,2,115.230 42257,0\O,4,1.41649921,1,113.1871631,7,-121.8826806,0\O,2,1.28195164,1 ,123.41661447,5,179.44676434,0\O,3,1.3775275,1,122.47355805,6,-179.281 32269,0\S,4,1.87361576,1,111.8749713,7,119.13311047,0\C,5,1.36318964,2 ,123.44545454,1,-0.29849994,0\Cl,5,1.75653209,2,117.47214039,12,179.82 921589,0\Cl,6,1.7541639,3,120.32194677,1,179.51507708,0\H,7,1.08280284 ,4,109.33924187,1,179.93467218,0\H,7,1.08309972,4,107.18210973,15,117. 73509895,0\H,7,1.07916032,4,111.48826877,15,-122.73099561,0\H,8,1.0126 8356,4,108.39740524,1,6.33840667,0\C,11,1.80866221,4,97.79784087,1,66. 14258581,0\H,10,0.97133208,3,111.00502497,1,-39.70418622,0\H,12,1.0698 9205,5,120.27528426,2,-179.97219346,0\H,19,1.07949525,11,106.25519656, 4,44.76253312,0\H,19,1.08005278,11,111.30530935,22,-119.69422493,0\H,1 9,1.08174442,11,108.92560816,22,118.82376558,0\\Version=SGI-G94RevD.1\ HF=-17398.0240946\RMSD=2.007e-04\Dipole=9.4475259,-10.235066,-23.44202 57\PG=C01 [X(C9H9Cl2O3S1)]\\@ SCIENCE AND PEACE WILL TRIUMPH OVER IGNORANCE AND WAR -- PASTEUR Job cpu time: 0 days 9 hours 12 minutes 7.4 seconds. File lengths (MBytes): RWF= 85 Int= 0 D2E= 0 Chk= 6 Scr= 1 Normal termination of Gaussian 94 ********************************************************* Dr. Michael Shokhen Senior researcher, Department of Biochemistry, G.S.Wise Faculty of Life Sciences, Tel-Aviv University, 69978, Tel-Aviv, Israel. Fax: 972-3-6415053 Email: shokhen@etgar.tau.ac.il ********************************************************* From chaudash@aston.ac.uk Tue Jun 17 09:49:33 1997 Received: from hermes.aston.ac.uk for chaudash@aston.ac.uk by www.ccl.net (8.8.3/950822.1) id IAA17351; Tue, 17 Jun 1997 08:53:46 -0400 (EDT) Message-Id: <199706171253.IAA17351@www.ccl.net> Received: from Pharm9.aston.ac.uk by hermes.aston.ac.uk with SMTP (PP); Tue, 17 Jun 1997 13:54:47 +0100 Comments: Authenticated sender is From: chaudash Organization: aston.ac.uk To: chemistry@www.ccl.net Date: Tue, 17 Jun 1997 14:00:44 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: modelling of inorganic compounds Reply-to: chaudash@aston.ac.uk Priority: normal References: <33A1A685.41C6@mmad1.pmmp.uic.edu> X-mailer: Pegasus Mail for Windows (v2.53/R1) Hello everyone, I joined the mailing list last week. I am working on modelling of organo-metallic compounds, in particular Al 3+ and Fe3+ compounds. I have used both semi empirical and ab-initio calculations for the Al3+ compounds and ab-initio for the Fe3+ compounds using effective core potentials (SBK)(producing some very anomalous geometric results). Has anyone had any experience of this type of modelling? I am relatively new to this field and would be most grateful for any advice. Thanks Shaqil. RSVP chaudash@aston.ac.uk From nauss@beryllium.crs.uc.edu Tue Jun 17 10:22:22 1997 Received: from beryllium.crs.uc.edu for nauss@beryllium.crs.uc.edu by www.ccl.net (8.8.3/950822.1) id JAA17591; Tue, 17 Jun 1997 09:20:27 -0400 (EDT) Received: (from nauss@localhost) by beryllium.crs.uc.edu (8.8.5/8.8.5) id JAA14535 for chemistry@www.ccl.net; Tue, 17 Jun 1997 09:20:24 -0400 (EDT) From: nauss@beryllium.crs.uc.edu (Jeffrey L. Nauss) Message-Id: <9706170920.ZM14533@beryllium.crs.uc.edu> Date: Tue, 17 Jun 1997 09:20:24 -0400 In-Reply-To: Alexandre Hocquet "CCL:semantics : molecular modelling" (Jun 16, 5:52pm) References: <9706162152.AA08009@tamarugo.cec.uchile.cl> Organization: Dept. Chemistry, University of Cincinnati Reply-to: Jeffrey.Nauss@UC.Edu X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:semantics : molecular modelling Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jun 16, 5:52pm, Alexandre Hocquet wrote: > the words "molecular modelling" still appear confusing to me : The question of the "proper" definition (if such a thing exists) for the term "molecular modelling" is an interesting one and one that has bothered me for some time as well. So I will offer my thoughts on the matter. > While it seems logical to think that "molecular modelling" is that part > of "computational chemistry" that describes behaviour of molecules by > the formalism of some theoretical model, there seems to exist in the > community a much more restrictive use of "molecular modelling". > This second definition could be "Use of any non quantum mechanics model > to describe the behaviour of molecules". The immediate question that comes into my mind with Alexandre's statement is: what is "computational chemistry?" Why is there a distinction between computational chemistry and molecular modelling? I have resolved the issue in my own mind as follows. Computational chemistry would be the application of numerical calculations to the study of molecular structure. Thus I would include in that definition ab initio, semi-empirical, AND empirical calculations. On the other hand, I consider molecular modelling to be a much more general term. Molecular modelling would be the application of some form of a model to studying molecular structure. It would include computational chemistry but also hand-held CPK models and simple drawings on paper. Thus, as I explain in my molecular modelling lectures, Pauling's discovery of the alpha helix was an example of molecular modelling. All he did (according to legend, at least) was wrap a strip of paper around a pencil. Simple and primitive, yet it *was* a model of a molecular. Another classic example was the discovery of the DNA double helix. Using simple metal templates and rods, Watson and Crick constructed a model of a molecule that answered many questions about the properties of DNA. Thus I consider computational chemistry to be a subset of the more general field of molecular modelling. Molecular modelling in itself may not involve any computations. But computational chemistry must. I wonder if one could trace the initial usage of the terms. -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss@UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss From roberto@viol.rockefeller.edu Tue Jun 17 10:49:30 1997 Received: from viol.rockefeller.edu for roberto@viol.rockefeller.edu by www.ccl.net (8.8.3/950822.1) id JAA17818; Tue, 17 Jun 1997 09:59:02 -0400 (EDT) Received: (from roberto@localhost) by viol.rockefeller.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id JAA09968 for chemistry@www.ccl.net; Tue, 17 Jun 1997 09:54:39 -0400 From: roberto@viol.rockefeller.edu (Roberto Sanchez) Message-Id: <199706171354.JAA09968@viol.rockefeller.edu> Subject: ** ANNOUNCING NEW VERSION OF MODELLER-4 To: chemistry@www.ccl.net Date: Tue, 17 Jun 1997 09:54:39 -0400 (PDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit ANNOUNCEMENT A NEW VERSION OF MODELLER-4, A PROGRAM FOR COMPARATIVE PROTEIN STRUCTURE MODELING, IS RELEASED. Please see the README file below for how to get the program. New features include faster execution, a better manual, more robust modeling of protein structure. A Linux version is also available. Current users can use the same keyword as for version 3 (you can find it in your .cshrc file). There is no need to resend the licensing agreement. Best Wishes, Andrej Sali ------------------------------------------------------------------------------- A review of CASP2 that qualifies MODELLER: R.L. Dunbrack~Jr., D.L. Gerloff, M. Bower, X. Chen, O. Lichtarge & F.E. Cohen. Meeting review: the second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar California, December 13-16, 1996. Folding & Design 2, R27-R42, 1997. ------------------------------------------------------------------------------- MODELLER PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 4, June 15, 1997 Copyright(c) 1989-1997 Andrej Sali All Rights Reserved Written by Andrej Sali, Roberto Sanchez, and Azat Badretdinov Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Andrej Sali, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. Tel: +1-212-327-7550. Fax: +1-212-327-7540 (or 7974). E-mail: sali@rockvax.rockefeller.edu. URL: http://guitar.rockefeller.edu/. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. MODELLER can also do several other tasks, including multiple comparison of protein sequences and/or structures, clustering, and searching of sequence databases. The program is described in a 150-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to academic non-profit institutions. First, please use the anonymous ftp account on guitar.rockefeller.edu (IP 129.85.13.198) to copy at least the following files from the pub/modeller directory to your computer: the license form (PostScript file academic-license.ps), the distribution file that contains the data files necessary to run MODELLER (modeller4-data.tar.Z), and an executable for each machine type that you want to use (described in file INSTALLATION). Next, please sign, and mail or fax the license form to Andrej Sali. You will then receive the key (MODELLER_KEY) that has to be assigned to the environment variable KEY_MODELLER4 in your login script (.cshrc). See file INSTALLATION for installation instructions. There is also a MODELLER home page on World Wide Web at URL http://guitar.rockefeller.edu that can be used to ftp the program and view the manual. A graphical interface to MODELLER is available as part of QUANTA, InsightII, and WEBLab, interactive molecular modeling programs with many tools for protein modeling and structural analysis. QUANTA, InsightII, and WEBLab facilitate preparation of input files for MODELLER (eg, alignment file) as well as an analysis of results (eg, an evaluation of the models). If you are interested in these programs, please contact Ms. Brenda Pfeiffer, Molecular Simulations Inc., 9685 Scranton Road, San Diego, CA 92121-3752, tel: +1-619-546-5319, fax: +1-619-458-0136, email: blp@msi.com. ** CONTENTS: src\ sources or executables for MODELLER; modlib\ libraries and data files for the programs; scripts\ script files used to compile and use MODELLER; doc\ MODELLER documentation; Makefile Makefile for compiling/installing MODELLER modules; modeller4.README this file; INSTALLATION how to install MODELLER; Install compilation and installation script relying on Makefile; examples\ examples; ------------------------------------------------------------------------------- Posted to: bionet.molec-model bionet.software bionet.structural-nmr bionet.xtallography bionet.software.source bionet.molbio.proteins bionet.biophysics bionet.announce ------------------------------------------------------------------------------- From TCUNDARI@LATTE.MEMPHIS.EDU Tue Jun 17 12:52:52 1997 Received: from latte.memphis.edu for TCUNDARI@LATTE.MEMPHIS.EDU by www.ccl.net (8.8.3/950822.1) id MAA19146; Tue, 17 Jun 1997 12:06:10 -0400 (EDT) From: Received: from LATTE.MEMPHIS.EDU by LATTE.MEMPHIS.EDU (PMDF V5.1-8 #16781) id <01IK6DFF9PES95PI38@LATTE.MEMPHIS.EDU> for chemistry@www.ccl.net; Tue, 17 Jun 1997 11:00:33 CST Date: Tue, 17 Jun 1997 11:00:33 -0600 (CST) Subject: Re: CCL:modelling of inorganic compounds To: chaudash@aston.ac.uk Cc: chemistry@www.ccl.net Message-id: <01IK6DFF9PEU95PI38@LATTE.MEMPHIS.EDU> X-VMS-To: IN%"chaudash@aston.ac.uk" X-VMS-Cc: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII The following two reviews deal specifically with SBK ECPs. 1) 41 - "Effective Core Potential Approaches to Computational Inorganic Chemistry;" M. T. Benson, T. R. Cundari, M. L. Lutz, S. O. Sommerer "Reviews in Computational Chemistry;" D. Boyd; K. Lipkowski (Eds.) 1996, 8, 145 - 202 (invited). 2) 34 - "Effective Core Potential Studies of Transition Metal Chemistry;" T. R. Cundari; M. S. Gordon Coord. Chem. Rev. 1996, 147, 87 - 115. This review provides an excellent overview of ECP applications in TM chemistry. Frenking, G.; Antes, I.; B From cyrillo@ifi.unicamp.br Tue Jun 17 12:58:22 1997 Received: from ifi.unicamp.br for cyrillo@ifi.unicamp.br by www.ccl.net (8.8.3/950822.1) id MAA19310; Tue, 17 Jun 1997 12:25:33 -0400 (EDT) Received: from polimero.ifi.unicamp.br (polimero.ifi.unicamp.br [143.106.6.16]) by ifi.unicamp.br (8.8.5/8.8.5) with ESMTP id NAA20276 for ; Tue, 17 Jun 1997 13:23:14 -0300 (EST) Received: (from cyrillo@localhost) by polimero.ifi.unicamp.br (8.6.9/8.6.9) id NAA13905 for CHEMISTRY@www.ccl.net; Tue, 17 Jun 1997 13:23:38 -0300 From: Marcio Cyrillo - pos Message-Id: <199706171623.NAA13905@polimero.ifi.unicamp.br> Subject: hyperchem x mopac6 To: CHEMISTRY@www.ccl.net Date: Tue, 17 Jun 1997 13:23:36 -0300 (BSC) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Dear Netters Could someone comment on this ? We are running a HYPERCHEM program (Version 4) and comparing the obtained results with the ones from MOPAC6 (unix version). The results are different, with the hyper' results systematically lower than MOPAC's. The numbers from MOPAC match the published Am1 results by Dewar et al. (JACS 1985, v107, pp3902). Any help will be greatly appreciated. Thanks in advance for your help. Sincerely yours Marcio Cyrrillo =-------------------------------------------------= Marcio Cyrillo - http://www.ifi.unicamp.br/~cyrillo Graduate Student State University of Campinas - Unicamp Campinas - SP - Brazil Applied Physics Department room 82 - phone +55 19 788 2383 home: +55 19 234 3494 From TCUNDARI@LATTE.MEMPHIS.EDU Tue Jun 17 13:04:10 1997 Received: from latte.memphis.edu for TCUNDARI@LATTE.MEMPHIS.EDU by www.ccl.net (8.8.3/950822.1) id MAA19229; Tue, 17 Jun 1997 12:19:03 -0400 (EDT) From: Received: from LATTE.MEMPHIS.EDU by LATTE.MEMPHIS.EDU (PMDF V5.1-8 #16781) id <01IK6DY7GA5C95PI38@LATTE.MEMPHIS.EDU> for chemistry@www.ccl.net; Tue, 17 Jun 1997 11:13:22 CST Date: Tue, 17 Jun 1997 11:13:22 -0600 (CST) Subject: Re: CCL:modelling of inorganic compounds To: chaudash@aston.ac.uk Cc: chemistry@www.ccl.net Message-id: <01IK6DY7GXOY95PI38@LATTE.MEMPHIS.EDU> X-VMS-To: IN%"chaudash@aston.ac.uk" X-VMS-Cc: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII The following reviews deal specifically with the application of the SBK ECPs to TM chemistry... 1) Cundari, T. R.; Gordon, M. S. Coord. Chem. Rev. 1996, 87, 87. 2) M. T. Benson, T. R. Cundari, M. L. Lutz, S. O. Sommerer "Reviews in Computational Chemistry;" D. Boyd; K. Lipkowski (Eds.) 1996, 8, 145 . The following is an excellent analysis of the application of ECPs in TM chemistry... 3) Frenking, G.; Antes, I.; Bohme, M.; Dapprich, S.; Ehlers, A. W.; Jonas, V.; Neuhaus, A.; Otto, M.; Stegmann, R.; Veldkamp, A.; Vyboishchikov, S. F. in "Reviews in Computational Chemistry;" Boyd, D. B.; Lipkowitz, K., Eds., VCH: New York, 1996, p. 63. The following are a tad older, but still excellent overviews of the challenges and opportunities (including ECPs) in comp TM chemistry 4) "The Challenge of d- and f-Electrons;" MC Zerner, D Salahub, Eds. ACS: Washington, D. C., 1989. 5) "Quantum Chemistry: The Challenge of Transition Metals and Coordination Chemistry;" A Veillard, Ed., Reidel: Dordrecht, 1986. Morokuma and Koga have a nice paper in Chem. Rev. focusing on applications, but for the life of me I can't find the reference. It was published in the late 80's or early 90's, I think. All these reviews have references to the too numerous to mention important contributions by other groups. Tom Cundari Associate Professor of Chemistry From Steve.Bowlus@sandoz.com Tue Jun 17 13:49:47 1997 Received: from gatekeeper.sandoz.att.nl for Steve.Bowlus@sandoz.com by www.ccl.net (8.8.3/950822.1) id MAA19558; Tue, 17 Jun 1997 12:51:14 -0400 (EDT) From: Received: by gatekeeper.sandoz.att.nl; id SAA01060; Tue, 17 Jun 1997 18:51:14 +0200 (MET DST) X400-Originator: Steve.Bowlus@sandoz.com X400-Recipients: CHEMISTRY@www.ccl.net X400-MTS-Identifier: [/PRMD=SANDOZ/ADMD=400NET/C=CH/;0034700005300244000002] X400-Content-Type: P2-1988 (22) Message-ID: <0034700005300244000002*@MHS> To: Subject: CCL: semantics: molecular modelling Date: Tue, 17 Jun 1997 18:51:50 +0200 WRT Jeffrey Nauss's query on tracking origin of the terms "computational chemistry" and "molecular modelling": There is a series of essays by Richard Counts in early volumes of J. Comput.- Aided Mol. Design on the "Computational Perspective", including one "Where Can I Find a Computational Chemist?", 1991, 5 (3), 273-274. Illuminating, perhaps especially to those who have been doing "molecular modeling" since before the term "computational chemistry" was invented. . . sb From Lutz.Ehrlich@EMBL-Heidelberg.de Tue Jun 17 13:53:52 1997 Received: from stork.EMBL-Heidelberg.DE for Lutz.Ehrlich@EMBL-Heidelberg.de by www.ccl.net (8.8.3/950822.1) id NAA19808; Tue, 17 Jun 1997 13:16:07 -0400 (EDT) Received: from cuckoo.embl-heidelberg.de (cuckoo.EMBL-Heidelberg.DE [192.54.41.16]) by stork.EMBL-Heidelberg.DE (8.8.4/8.8.4) with ESMTP id TAA15771 for ; Tue, 17 Jun 1997 19:16:07 +0200 (MDT) Received: by cuckoo.embl-heidelberg.de (8.7.1) id RAA08940; Tue, 17 Jun 1997 17:16:05 GMT Date: Tue, 17 Jun 1997 19:16:05 -6000 From: Lutz Ehrlich To: chemistry@www.ccl.net Subject: Simplified residue models (off-lattice) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I'm studying the possible mixing of all-atom and simplified residue models (off-lattice) in protein MD simulations. I would be very grateful if anybody could point me to references regarding such simplified residue models. I'll post a summary ASAP. Thanks in advance, Lutz Ehrlich --------------------- Lutz Ehrlich Structural Biology EMBL Meyerhofstr. 1 D-69012 Heidelberg Germany email: lutz.ehrlich@embl-heidelberg.de web : http://www.embl-heidelberg/~ehrlich phone: +49-6221-387-140 fax : +49-6221-387-517 From d3g359@fido.pnl.gov Tue Jun 17 14:49:34 1997 Received: from pnl.gov for d3g359@fido.pnl.gov by www.ccl.net (8.8.3/950822.1) id OAA20528; Tue, 17 Jun 1997 14:25:03 -0400 (EDT) Received: from fido.pnl.gov by pnl.gov (PMDF V5.1-7 #21283) with SMTP id <01IK6EDSLNJ491YTMA@pnl.gov> for CHEMISTRY@www.ccl.net; Tue, 17 Jun 1997 11:24:59 PDT Received: by fido.pnl.gov (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for CHEMISTRY@www.ccl.net id LAA23849; Tue, 17 Jun 1997 11:20:49 -0700 Date: Tue, 17 Jun 1997 11:20:49 -0700 From: d3g359@fido.pnl.gov (John Nicholas) Subject: Theoretical study of methyl migrations To: CHEMISTRY@www.ccl.net Message-id: <199706171820.LAA23849@fido.pnl.gov> Hi, I'm looking for information on theoretical studies of methyl migrations in hydrocarbons. Given a carbon with four distinct substituents (X)(Y)C(H)(CH3), I'd like to know the transition state for flipping the H and CH3. Another way of thinking of this is given an assymetric ring with a methyl on one "side", how does it migrate to the other side. Any ideas or references would be greatly appreciated. BTW, a search of Current Contents didn't turn up anything interesting. I try not to ask these questions before looking to the obvious sources. ------------------------------------------------------------------------------ John Nicholas Office: (509) 375-6559 Senior Research Scientist FAX: (509) 375-6631 Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Mailstop K1-96 Richland, WA 99352 ------------------------------------------------------------------------------ From bianco@lord.Colorado.EDU Tue Jun 17 14:55:19 1997 Received: from lord.Colorado.EDU for bianco@lord.Colorado.EDU by www.ccl.net (8.8.3/950822.1) id OAA20459; Tue, 17 Jun 1997 14:15:29 -0400 (EDT) Received: by lord.Colorado.EDU (920330.SGI/911001.SGI) for CHEMISTRY@www.ccl.net id AA04275; Tue, 17 Jun 97 12:12:39 -0600 From: bianco@lord.Colorado.EDU (Roberto Bianco) Message-Id: <9706171812.AA04275@lord.Colorado.EDU> Subject: Re: CCL:MCSCF / selection of configurations To: CHEMISTRY@www.ccl.net Date: Tue, 17 Jun 1997 12:12:38 -0600 (MDT) X-Mailer: ELM [version 2.4ME+ PL26 (25)] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi all! A few week ago I posed the following question: --- I would like to do a state-averaged MCSCF calculation for the first few electronic states of a relatively large system. Are there references about the possible strategies one could use to select the relevant configurations for my particular case ? --- I am grateful to Johannes Weber for his useful reply, attached below. Roberto -- Roberto Bianco / Department of Chemistry & Biochemistry University of Colorado / Campus Box 215 / Boulder, CO 80309 / USA bianco@lord.colorado.edu / phone +(303) 492-3504 / fax +(303) 492-5894 ----- Forwarded message from Johannes Weber ----- From Johannes.Weber@Uni-Koeln.DE Thu May 29 12:50:05 1997 Date: Thu, 29 May 1997 20:52:01 +0200 (MST) From: Johannes Weber To: Roberto Bianco Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:MCSCF / selection of configurations In-Reply-To: <9705271714.AA04277@lord.Colorado.EDU> Message-Id: Dear Roberto! On Tue, 27 May 1997, Roberto Bianco wrote: > > I would like to do a state-averaged MCSCF calculation for the first few > electronic states of a relatively large system. > > Are there references about the possible strategies one could use to > select the relevant configurations for my particular case ? You didn't mention what kind of MCSCF calculation you want do and you didn't specify the molecule either, so my answer can't be very specific. In my opinion it seems to be quite difficult to treat 'a relative large system' with MCSCF at all (just depends on the word 'relative'). For a detailed overview of MCSCF methods you might look at R. Shepard, Adv. Chem. Phys. _69_, 63 (1987). In the CASSCF method (mostly used) you choose active molecular orbitals (MO's) instead of configurations. If you want an overview to CASSCF and some examples for choosing the active space (dealing with rather small molecules) look at B.O. Roos in 'Lecture Notes in Quantum Chemistry', Springer, Berlin (1992). (There must be a review about CASSCF somewhere in a journal.) A more general but very instructing source for choosing configurations within the CI method (similar criteria as in MCSCF) is I. Shavitt in Schaefer III, 'Modern Theoretical Chemistry', Vol.3, Chap. 6, Plenum Press, New York (1977). CASSCF/CASPT2 calculations of excited states on a 'larger' molecule (Biphenyl, C12H10) were done by M. Rubio, M. Merchan, E.Orti, B.O. Roos, Chem. Phys. Lett. _234_, 373 (1995). (Biphenyl, C12H10) Just look in the section 'details of calculation' to find out the authors strategies. The essence is, that MCSCF (or more precisely CASSCF) isn't a 'black box' method, so one must combine observation of the MO's (it's fine if you have NO's and occupation numbers) with chemical intuition (e.g. selecting pi-MO's in aromatic compounds) and - last but not least - some stamina in doing test calculations to find out the proper MO's or configurations. Hope it helps, Johannes. ---------------------------------------------------------------------- | Johannes Weber | Johannes.Weber@uni-koeln.de | | Institut fuer Physikalische Chemie | fax: 0049-(0)221-470-5144 | | Lehrstuhl Prof. Dr. G. Hohlneicher | tel: 0049-(0)221-470-4816 | | Universitaet zu Koeln | | ---------------------------------------------------------------------- ----- End of forwarded message from Johannes Weber -----