From san@mbu.iisc.ernet.in Tue Oct 4 01:17:02 1994 Received: from sangam.ncst.ernet.in for san@mbu.iisc.ernet.in by www.ccl.net (8.6.9/930601.1506) id BAA19757; Tue, 4 Oct 1994 01:12:18 -0400 From: Received: from soochak.ncst.ernet.in (soochak.ncst.ernet.in [144.16.11.100]) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with ESMTP id KAA23995 for ; Tue, 4 Oct 1994 10:41:40 +0500 Received: from nic.iisc.ernet.in (twisha.ece.iisc.ernet.in [144.16.64.4]) by soochak.ncst.ernet.in (8.6.8.1/8.6.5) with SMTP id KAA02588 for ; Tue, 4 Oct 1994 10:40:41 +0530 Received: by nic.iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA05544; Tue, 4 Oct 94 10:45:27 EST Date: Tue, 4 Oct 94 10:45:27 EST Message-Id: <9410041545.AA05544@nic.iisc.ernet.in> Received: by vigyan.iisc.ernet.in (smail2.3) id AA00683; 4 Oct 94 10:22:58 EST (Tue) To: vigyan!chemistry@ccl.net Subject: code for helical wheel plot Hi friends, Some time ago i offered to give the code for a program which will generate the coordinates for helix wheel given a sequence of alpha helix. since i recieved a large no. of requests from the people asking for such a program, i have decided to post it to the CCL . Please take this program from here. Since it would require me spend a lot of time for individual postings, i hope CCL will be convenient to all of us. About the program: This is a very very simple fortran program. It takes an initial arbit point with (r,phi,z) as (10,0,0) and keeps on rotating this point by 100 deg. for each amino acid in the seq. It increase the radius of circle by 5 every 18 residues to avoid overlapping of the points. INPUT : input to this program is in SINGLE letter code of amino acids in format (40(1x,a1)) Outpot : Output lists the amino acid in SINGLE letter code and Coordinates associated with it in a format that is analogous to PDB format. The format of the output is (13x,a1,16x,3f8.3). *********start of the code******************************************** c program helical wheel c it generate the coordinates for plotting a helical wheel for c given sequence of the helix. Method is from c schiffer & Edmundson, Biophyscal J. (1967). c maximum length of helix taken is 40 Amino acids parameter (i=50) character*1 r dimension r(i),x(i),y(i),z(i) dimension rad(i),phi(i) open (unit=1,file='hel.inp') open (unit=2,file='hel.out') 10 format (40(1x,a1)) 11 format (13x,a1,16x,3(f8.3)) read(1,10) (r(j),j=1,40) rad(1)=10.0 phi(1)=0.0 z(1)=0.0 k=1 do j=2,40 if (r(j).ne.' ') then k=k+1 if (j.le.18) rad(j)=rad(1) if ((j.gt.18).and.(j.le.36)) rad(j)=rad(1)+5.0 if (j.gt.36) rad(j)=rad(1)+10.0 phi(j)=phi(j-1)+100.0 if(phi(j).ge.360.0) phi(j)=phi(j)-360.0 z(j)=0.0 endif enddo pi=acos(-1.0)/180.0 do j=1,k phi(j)=pi*phi(j) x(j)=rad(j)*cos(phi(j)) y(j)=rad(j)*sin(phi(j)) write(2,11) r(j),x(j),y(j),z(j) enddo stop end  ********end of the code *********************************************** users can change the code at the will and pass it on to whomever they wish. This coordinates from this program can visualized in any graphics program .e.g. DTMM (DeskTop Molecular Modellar) and pltted. In case any body finds a bug in the program, please send a mail to me at san@mbu.iisc.ernet.in sandeep kumar From cosgrove@zeneca-ph.co.uk Tue Oct 4 05:17:06 1994 Received: from eros.britain.eu.net for cosgrove@zeneca-ph.co.uk by www.ccl.net (8.6.9/930601.1506) id FAA21034; Tue, 4 Oct 1994 05:12:14 -0400 Received: from zeneca-ph.co.uk by eros.britain.eu.net with UUCP id ; Tue, 4 Oct 1994 10:11:48 +0100 From: Dave Cosgrove Date: Tue, 4 Oct 94 10:13:19 GMT Message-Id: <13396.9410041013@iciukph.zeneca-ph.co.uk> Received: from zeneca by iciukph.zeneca-ph.co.uk; Tue, 4 Oct 94 10:13:19 GMT To: chemistry@ccl.net In-Reply-To: <9410031206.ZM14065@still3.chem.columbia.edu> (message from Peter Shenkin on Mon, 3 Oct 1994 12:06:04 -0400) Subject: Re: CCL:recycling old computers... > Subject: CCL:recycling old computers... > I recently "inherited" two Evans & Sutherland PS330 systems. > I'm trying to figure out the best possible use of these > once mighty dinosaurs.... Since they put out a fair amount of heat, they could be useful in those instances where an electric fire plugged in would arouse unfavourable comment. From acklin@chbs.CIBA.COM Tue Oct 4 09:17:17 1994 Received: from chsun.eunet.ch for acklin@chbs.CIBA.COM by www.ccl.net (8.6.9/930601.1506) id IAA22037; Tue, 4 Oct 1994 08:55:57 -0400 Received: from Ciba-GW.CHBS.CIBA.COM by chsun.eunet.ch (8.6.4/1.34) id MAA14353; Tue, 4 Oct 1994 12:00:28 +0100 Received: from Central.CHBS.CIBA.COM by Ciba-GW.CHBS.CIBA.COM (4.1/Ciba2.0-R1.0) id AA14870; Tue, 4 Oct 94 12:00:20 +0100 Received: from camm1.ph.chbs by Central.CHBS.CIBA.COM id AA05703; Tue, 4 Oct 1994 11:59:50 +0100 (5.65c8/Ciba2.0-C1.1) Received: by camm1.ph.chbs (931110.SGI/930416.SGI/camm.ph.chbs-1.0) for @cgchm.is.chbs:chemistry@ccl.net id AA17108; Tue, 4 Oct 94 12:02:02 +0100 Date: Tue, 4 Oct 94 12:02:02 +0100 From: acklin@chbs.CIBA.COM (Dr.Pierre Acklin) Message-Id: <9410041102.AA17108@camm1.ph.chbs> To: chemistry@ccl.net Subject: iron basis set Dear Netters, I am trying to model iron complexes with round about 30 heavy atoms. Introducing special angular and torsional constraints into amber force field calculation in MacroModel leads to good and reproducable geometry predictions. Geometry predictions are ok as they allow to discriminate between molecules which can form chelate complexes and those, which can't. Nevertheless it would be very helpful for the project, if some kind of energy or stability predictions would be possible. This makes me ask you the following questions: Is it possible to treat iron complexes with more than 30 heavy atoms in an ab initio program like Gaussian in a reasonable time on a SGI workstation? Are there any basis sets and references therefore available to handel iron in Gaussian92 or DFT on a better level than sto-3g? How good are results of semi empirical calculations form Ampac or Zindo in terrms of energy and geometry? I'll be glad to summarise the responses for the list. Pierre ========================================== Dr.Pierre Acklin CIBA-GEIGY AG K-136.P.13 CH-4002 Basel acklin@chbs.ciba.com ++41 61 696 23 62 ++41 61 696 23 75 ========================================== From chemdcl3@emrycc.cc.emory.edu Tue Oct 4 12:17:18 1994 Received: from emoryu1.cc.emory.edu for chemdcl3@emrycc.cc.emory.edu by www.ccl.net (8.6.9/930601.1506) id LAA29616; Tue, 4 Oct 1994 11:19:10 -0400 Received: from emrycc.cc.emory.edu by emoryu1.cc.emory.edu (5.65/Emory_cc.4.0.1) via SMTP id AA28699 ; Tue, 4 Oct 94 11:19:03 -0400 Message-Id: <9410041519.AA28699@emoryu1.cc.emory.edu> Date: 4 Oct 94 11:19:00 EST From: "DR. LIOTTA" Subject: CCL:Radicles To: "chemistry" I'm looking for information about finding radicle transition states using MOPAC and GAUSSIAN92. My system contains SiH3. and C. radicles. Thank you, V. Cornel From bishop@lisboa.ks.uiuc.edu Tue Oct 4 12:22:11 1994 Received: from lisboa.ks.uiuc.edu for bishop@lisboa.ks.uiuc.edu by www.ccl.net (8.6.9/930601.1506) id LAA00621; Tue, 4 Oct 1994 11:32:29 -0400 Received: from helsinki by lisboa.ks.uiuc.edu (NX5.67d/NX3.0M) id AA03821; Tue, 4 Oct 94 10:33:56 -0500 From: Tom Connor Bishop Message-Id: <9410041533.AA03821@lisboa.ks.uiuc.edu> Received: by helsinki.ks.uiuc.edu (NX5.67d/NX3.0X) id AA02821; Tue, 4 Oct 94 10:33:55 -0500 Date: Tue, 4 Oct 94 10:33:55 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@ccl.net Subject: summary molec surfs Reply-To: bishop@lisboa.ks.uiuc.edu Dear netters, here's a summary of the responses i obtained for the posting. ==>Dear netters, ==>i'm looking for references to algorithms (not programs) ==>which are used to calculate molecular surfaces, (vdW,elect...etc). ==>We wish to include this as a feature in our own molecular graphics ==>package. ==> ==>Please send any refs that you have to me and i will summarize a list ==>to the net. ==> ==>thanks in advance. ==>tom thanks to all who responded. i did not check for redundancies. tom ***************************************************************** From: "Richard Bone" Hi, I'm attaching some references for molecular surfaces. Some of the really obvious ones (e.g., Richards, Connolly, etc., are missing but I expect that everyone else will send you those!) Yours Richard Bone Computational Chemist Terrapin Technologies, Inc. South San Francisco USA E-mail : rgab@trpntech.com __________________________________________________________ Molecular Surfaces: Calculation and Computation [] ÒAn Algorithm for the Representation and Computation of Supermolecular Surfaces and VolumesÓ, H. R. Karfunkel and V. Eyraud J. Comp.-Chem., 10, 629, (1989) [] ÒOn the Analytical Calculation of van der Waals Surfaces and Volumes: Some Numerical AspectsÓ, M. Petitjean J. Comp. Chem., 15, 507, (1994) [] ÒSurface and volume of three, four, six and twelve hard fused spheresÓ, R. Lustig Molec. Phys., 55, 305, (1985) [] ÒExact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radiiÓ, K. D. Gibson and H. A. Scheraga Molec. Phys., 62, 1247, (1987) [] ÒSpheres, Molecules and Hidden Surface RemovalÓ, D. Halperin and M. H. Overmars [Submitted for Publication], (1994) [] ÒRapid Approximation to Molecular Surface Area via the Use of Boolean Logic and Look-Up TablesÓ, S. M. Le Grand and K. M Merz, Jr. J. Comp. Chem., 14, 349, (1993) [] ÒPlotting protein surfacesÓ, M. L. Connolly J. Molec. Graph., 4, 93, (1986) [] ÒGEPOL: An Improved Description of Molecular Surfaces. I. Building the Spherical Surface SetÓ, J. L. Pascual-Ahuir and E. Silla J. Comp. Chem., 11, 1047, (1990) [] ÒGEPOL: An Improved Description of Molecular Surfaces. II. Computing the Molecular Area and VolumeÓ, E. Silla J. L., I–aki Tu–—n and Pascual-Ahuir J. Comp. Chem., 12, 1077, (1991) [] ÒMolecular Mechanics and Molecular Shape. V. On the Computation of the Bare Surface Area of MoleculesÓ, A. Y. Meyer J. Comp. Chem., 9, 18, (1988) [] ÒImproved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational EfficiencyÓ, F. Eisenhaber and P. Argos J. Comp. Chem., 14, 1272, (1993) [] ÒFast Generation of Molecular Surfaces from 3D Data Fields with an Enhanced ÔMarching CubeÕ AlgorithmÓ, W. Heiden, T. Goetze and J. Brickmann J. Comp. Chem., 14, 246, (1993) [] ÒThe molecular surface packageÓ, M. L. Connolly J. Molec. Graph., 11, 139, (1993) [] ÒA Vectorized Algorithm for Calculating the Accessible Surface Area of MacromoleculesÓ, H. Wang and C. Levinthal J. Comp. Chem., 12, 868, (1991) [] ÒA real-time malleable molecular surfaceÓ, T. E. Klein, C. C. Huang, E. F. Pettersen, G. S. Couch, T. E. Ferrin and R. Langridge J. Molec. Graph., 8, 16, (1990) [] ÒDescription of molecular surface shape using fourier descriptorsÓ, S. E. Leicester, J. L. Finney and R. P. Bywater J. Molec. Graph., 6, 104, (1988) [] ÒNumerical Computation of Surface Areas of MoleculesÓ, P. Senn J. Math. Chem., 6, 351, (1991) [] ÒApproximation and Characterisation of Molecular SurfacesÓ, B. S. Duncan and A. J. Olson Biopolymers., 33, 219, (1993) [] ÒTriangulation algorithms for the representation of molecular surface propertiesÓ, W. Heiden, M. Schlenkrich and J. Brickmann J. Comp.-Aided Molec. Des., 4, 255, (1990) [] ÒComputing Connolly SurfacesÓ, J.-D. Boissonnat, O. Devillers, J. Duquesne and M. Yvinec J. Molec. Graph., 12, 61, (1994) [] ÒSegmentation of protein surfaces using fuzzy logicÓ, W. Heiden and J. Brickmann J. Molec. Graph., 12, 106, (1994) [] ÒGradient discontinuities in calculations involving molecular surface areaÓ, R. J. Wawak, K. D. Gibson and H. A. Scheraga J. Math. Chem., 15, 207, (1994) [] ÒMolecular SurfacesÓ, P. G. Mezey Reviews in Computational Chemistry, Vol. I, p. 265, Ed. K. Lipkowitz and D. Boyd, VCH (1991) [] ÒMeasurement of protein surface shape by solid anglesÓ, M. L. Connolly J. Molec. Graph., 4, 3, (1986) Molecular Surfaces: Display, Matching and Comparison [] ÒMolecular surface comparison: Application to drug designÓ, F. Blaney, P. Finn, R. Phippen and M. Wyatt J. Molec. Graph., 11, 98, (1993) [] ÒA rapid method for comparing and matching the spherical parameter surfaces of molecules and other irregular objectsÓ, P. Bladon J. Molec. Graph., 7, 130, (1989) [] ÒGraphics visualisation of molecular surfacesÓ, S. R. Gadre and A. Taspa J. Molec. Graph., 12, 45, (1994) [] ÒShape Analysis of Molecular SurfacesÓ, B. S. Duncan and A. J. Olson J. Molec. Graph., 33, 231, (1993) [] ÒA Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining SitesÓ, M. Gerstein Acta Cryst., A48, 271, (1992) [] ÒTopological Analysis of Complex Molecular SurfacesÓ, C.-D. Zachmann, W. Heiden, M. Schlenkrich and J. Brickmann J. Comp. Chem., 13, 76, (1992) [] ÒDetermination of clefts in receptor structuresÓ, R. A. Lewis J. Comp.-Aided Molec. Des., 13, 133, (1989) [] ÒDetection of Cavities in a Set of Interpenetrating SpheresÓ, P. Alard and S. J. Wodak J. Comp. Chem., 12, 918, (1991) [] ÒSelf-Similarity of Solvent-Accessible Surfaces of Biological and Synthetical MacromoleculesÓ, C.-D. Zachmann, S. M. Kast, A. Sariban and J. Brickmann J. Comp. Chem., 14, 1290, (1993) [] ÒInteractive map projection algorithm for illustrating protein surfacesÓ, D. J. Barlow and J. M. Thornton J. Molec. Graph., 4, 97, (1986) ******************************************************************************* From: Jens.Sadowski@EROS.CCC.Uni-Erlangen.DE Dear Tom, here are some references for the calculation of molecular surfaces: Moon, J. B.; Howe, W. J. J. Mol. Graph. 1989, 7, 109. Pascual-Ahuir, J. L.; Silla, E. J. Comp. Chem. 1990, 11, 1047. Silla, E.; Tu~non, I.; Pascual-Ahuir, J. L. ibid. 1991, 12, 1077. Heiden, W.; Goetze, T.; Brickmann, J. J. Comp. Chem. 1993, 14, 246. Guerrero-Ruiz, G.; Ocadiz-Ramirez, A.; Gardu~no-Juarez, R. Computers Chem. 1991, 15, 351. Connolly, M. J. Appl. Cryst. 1985, 18, 499. Regards, Jens ******************************************************************************* From: beroza@scripps.edu (Paul Beroza) Michael Connolly has written several papers on such algorithms, eg. AUTHOR="Connolly, M. L.", JOURNAL="J. Appl. Cryst.", TITLE="Analytical Molecular Surface Calculation", VOLUME="16", PAGES="548-558", YEAR="1983" Paul ***************************************************************************** From: Andreas Windemuth Hi Tom, ... below is the description of pmd-surf, which can be compiled >from PMD. As for the algorithm, it is related to the Conolly algorithm for surface area (see reference below). I call it CIM, and it is presented (although not really described) in my paper on PMD. It is much faster than other complete analytical algorithms, but not as fast as the incomplete MSEED (reference below). See the PMD paper for a comparison. ..... Cheers, Andreas |===================================================== References: @article{CONO83, author={Michael L. Conolly}, title={Analytical Molecular Surface Calculation}, journal=JAC, volume=16, year=1983, pages={548--558}, keywords={Molecular surface, accessible surface, analytical surface, solvent accessible} } % @article{PERR92, author={G. Perrot and B. Cheng and K. D. Gibson and J. Vila and K. A. Palmer and A. Nayeem and B. Maigret and H. A. Scheraga}, title={{MSEED}: A Program for the Rapid Analytical Determination of Accessible Surface Areas and Their Derivatives}, journal=JCC, volume=13, year=1992, pages={1--11}, keywords={MSEED, Molecular surface, accessible surface, analytical surface, solvent accessible} } % @inproceedings{WIND95, author={Andreas Windemuth}, booktitle={Parallel Computing in Computational Chemistry}, editor={Timothy G. Mattson}, publisher={ACS Books}, year=1995, title={Advanced Algorithms for Molecular Dynamics Simulation: The Program PMD} } *************************************************************************** From: dodd@roebling.poly.edu (Lawrence R. Dodd) "Analytical treatment of the volume and surface area of molecules formed by an arbitrary collection of unequal spheres intersected by planes" L.R. Dodd and D.N. Theodorou MOLECULAR PHYSICS, Volume 72, Number 6, 20 April 1991, 1313-1345. {Fortran code available upon request.} From jamejias@obelix.cica.es Tue Oct 4 12:23:56 1994 Received: from obelix.cica.es for jamejias@obelix.cica.es by www.ccl.net (8.6.9/930601.1506) id LAA01731; Tue, 4 Oct 1994 11:46:49 -0400 From: Date: Tue, 4 Oct 94 16:46:30 +0100 Received: by obelix.cica.es (5.64/X1.00) id AA26305; Tue, 4 Oct 94 16:46:30 +0100 Message-Id: <9410041546.AA26305@obelix.cica.es> To: CHEMISTRY@ccl.net Subject: EPR Summary Hi again Last Saturday I posted the next questions concerning the calculation of spin density and prediction of EPR spectra from quantum mechanical calculations. ==================================================================== Dear Netters Can somebody answer those questions? 1) Is it possible to predict or at least to interpret EPR spectra from ab initio quantum mechanical calulations for radicals? 2) If so, is there software to do it from the information given by standard quantum chemical calculations codes? 3) Which kind of calculation is neccesary or recommended to calculate EPR spectra? Is it enough with Hartree-Fock calculations, say UHF, or is it neccesary to go beyond Hartree-Fock wavefuncion? 4) How good is the spin density given by UHF calculations when compared to that given by EPR? Please, answer directly to me. Of course, I shall summarize for the net. Thank you in advance Jose Antonio Mejias Romero Departamento de Quimica-Fisica Universidad de Sevilla. Spain e-mail: jamejias@obelix.cica.es ==================================================================== I have got several answers. All of them quite interesting. Jussi Eloranta wrote this ... ----------------------- > Can somebody answer those questions? > > 1) Is it possible to predict or at least to interpret EPR > spectra from ab initio quantum mechanical calulations > for radicals? > For simple systems, yes. > 2) If so, is there software to do it from the information > given by standard quantum chemical calculations codes? > I've done some calculations using gaussian 92. This outputs fermi contact terms which can be easily converted to coupling constants. GAMESS will also output this information. > 3) Which kind of calculation is neccesary or recommended > to calculate EPR spectra? Is it enough with Hartree-Fock > calculations, say UHF, or is it neccesary to go beyond > Hartree-Fock wavefuncion? Usually UHF does not give correct answers. I usually use CI calculations (singles and/or doubles subtitutions). Also you have to be very careful about the basis set you use. Once I also tried MP2 and it gave reasonable couplings in some cases. > 4) How good is the spin density given by UHF calculations > when compared to that given by EPR? UHF usually gives too high couplings (at least for PI radicals) but not always. Here is a short example I computed a while ago for CH and CH3 with different basis sets. This was just a quick test, so there may be errors in these tables. CH radical (G92) [QCISD with frozen core and optimization] Basis A1[G] E1[%] CPU[min] / iter expt -20.6 0.0 ---- DZ -26.470 22.2 0.79 dujineveldt -21.799 5.5 10.67 dujineveldt {X} -21.798 5.5 13.14 STO-3G -28.886 28.6 0.56 STO-6G -39.607 48.0 0.81 6-311G** -22.655 9.1 2.82 6-311G -24.577 16.2 1.33 tzp -22.124 6.9 2.33 tzplarge -23.853 13.6 2.67 {X} = no frozen core (ie. QCISD=FULL) CH3 radical (G92) [QCISD with frozen core and optimization] Basis A1[G] A2[G] A3[G] E1[%] E2[%] E3[%] CPU[min] /iter expt -25 -25 -25 0.0 0.0 0.0 --- DZ -35.87 -35.87 -35.87 30.3 30.3 30.3 1.29 dujineveldt -25.89 -25.89 -25.89 3.4 3.4 3.4 125 Also you may be interested in some utils I've written: cf.c Extract hyperfine couplings from G92 output file. convert.c Convert G82 basis set format to G92 basis set format. cplt.c Produce suitable ASCII files from G92 orbital output file for visualization. These and and converted GENBAS (from ccl.net) are available from epr.chem.jyu.fi via anonymous ftp. The directory is /pub/g92. I haven't tested any of these programs extensively, so watch out... Here are some references: About hyperfine coupling calculations: 1. D. M. Chipman, The spin polarization model for hyperfine coupling constants, Theor. Chim. Acta (1992), 82: 93-115. 2. D. Feller, E. McCullogh, Jr., A Comparison of Unrestricted HF and restricted open-shell HF-based methods for determining the magnetic hyperfine parameters of NO, J. Chem. Phys. (1993), 99: 2829-2840. 3. D. M. Chipman, Theoretical Study of the Properties of Methyl Radical, J. Chem. Phys. (1983), 78: 3112-3132. Quick intro to basis sets: x. J. K. Labanowski, OSC, Simplified Introduction to AB Initio Basis Sets. Terms and Notation. From anon. ftp server ccl.net. I hope this helps. Regards, Jussi Eloranta ----------------------- Me again: The paper by Chipman in Theor. Chim. Acta. gives a nice explanation of the spin polarization effect and how it is included in UHF and CI calculations. As those are ab initio methods you can see what you have and what is lacking in your calculations. Thus, you know why UHF gives usually wrong results and SCI for open shells uses to work ok. The relevance of the basis set as well as the dynamical correlation are also discussed. Summaryzing: it is well known how to obtain good spin densities from ab initio calculations. A different question is how expensive your calculation will be. I haven't still read the other references given by Jussi Eloranta but I shall read them as soon as I can. Of course I have had answers from people using DFT. Here you have one example ----------------------- Hi Jose Antonio, HF, and UHF usually lead to wrong spin densities. DFT, on the contrary, lead to much better spin densities at nucl, and EPR parameters in general. quite significant results have been obtained by Delley, and Noodelman in the past (at the time of the LDA approximation). ----------------------- Me again: I believe that DFT can work better than UHF for spin densities. But how can it be explained? Is it possible to see which contributions you include or which are lacking in your density function? Is it possible to know why and when some exchange-correlation potential fails? There are people who used ab initio as well as DFT calculations. ----------------------- Dear Sir, you have asked about the accuracy of spin density calculation with ab initio calculations. Since I have worked quite a while on that field let me give you some comments on it. First of all, spin density calculation have turned out to be quite problematic for ab initio calculations. This is mainly because of the local nature of Spin density (not because of the cusp, as you might hear). Or if you want to calculate the anisotropic part it is no problem but if you calculate the Fermi-Contact term you should go to really correct wave functions (best always MR-CI, but also CCSD(T) (QCISD(T)) will do it). Okay let us be something more concrete: UHF : Will give you between 3 to 10 times to large Fermi contact terms. UMPx: Improves it somewhat but is roughly comparable to UHF. QCISD(T),CCSD(T) will be accurate up to 5% as well as MR-CI, but with a little bit spezialized programs. So lets talk about basis sets. To say it simple the standard basis sets (DZP, 6-31G** and so on) will do a worse job for that property. This is relatively easy to believe, since they have been optimized in the valence region. So you should add a diffuse function and a "peak" function to your standard basis sets. The work of Chong et al., and Chipman may be taken as citation for that. This corrects the basis set to acceptable flexibility. Good, there is one possible way out if you do not want to go to CCSD(T) or MR-CI calculation. If you take density functionals (say gradient corrected ones) you will be more or less accurate, dependening a little bit on the Functional and much more on the kind of Center. For example beta protons you have quite correct values, but the center were you have your spin is to small by about a factor 2. This is mainly because direct and indirect effects have been somewhat unbalanced teated. This may change by other functionals I can only say it for the so called BLYP and BVWN functionals. It should appear a publication of that from miself in Chem.Phys.Lett. were you should also find some references back mainly from Eriksson and Barone et al. who have used this method extensively. Other literature which I would recommend: D. Feller and E.R. Davidson, J.Chem.Phys. 88 (1988) 7580 D. Feller and E.R. Davidson, in "Theoretical Models of Chemical Bondings", ed. Z.B. Maksic, Springer, Berlin. H.U. Suter and B. Engels, J.Chem.Phys, 100 (1994) 2936. and the references therein where you should find the other important contributions from Chipman, Carmichael and Wong. hope this gives a little impression, Hans Ulrich Suter, Centro Svizzero di Calcolo Scientiifico CH-6928 Manno. ----------------------- Me again: The chapter by Feller and Davidson in "Theoretical Models..." gives an excellent review about the key points to consider in order to calculate spin density. Here you have another interesting mail about ab initio and DFT calculations. Here again I have the impression that with ab initio you know what you have and with DFT you try it until you get a good result. ----------------------- Jose, > > Can somebody answer those questions? > > 1) Is it possible to predict or at least to interpret EPR > spectra from ab initio quantum mechanical calulations > for radicals? > > 2) If so, is there software to do it from the information > given by standard quantum chemical calculations codes? > > 3) Which kind of calculation is neccesary or recommended > to calculate EPR spectra? Is it enough with Hartree-Fock > calculations, say UHF, or is it neccesary to go beyond > Hartree-Fock wavefuncion? > > 4) How good is the spin density given by UHF calculations > when compared to that given by EPR? > Sorry to take so long, but two small children prevent me from stringing together two minutes of rational thought on the weekends. Your question has two interpretations, as I see it. Either you want to simulate actual spectra by feeding in necessary coupling constants, etc., or you want to calculate those constants (or maybe both). I can't help much with the former. I seem to recall QCPE has a spectral fitting/reproduction program for EPR, but I've never used it. I know more about the prediction of hyperfine splittings from QM wavefunctions. We recently compared UHF, PUHF and MP2 spin densities for the prediction of isotropic hfs values in 25 different radicals (all containing phosphorus) for several different magnetically active nuclei. We are in the progress of repeating this work with ROHF and DFT spin densities. My bottom line analysis at this point, based on this and several other studies we have performed earlier (as well as the literature) is as follows: 1) Multireference CI with large, uncontracted basis sets gives great results, but is obviously limited to VERY small systems (see work of Knight, Davidson, and Feller, primarily -- also Chipman, Carmichael, and Barone) Finite field calculations with other sophisticated levels of theory (MP4, CCSD(T), BD, etc.) are similarly good for these small systems -- same groups primarily. 2) MP2 densities give what we regard as the best compromise between accuracy and speed when moderate basis sets are used, e.g., Pople's 6-311G** (diffuse functions seem unnecessary in most cases we have examined, even anions). There is almost certainly a fortuitous cancellation of errors with such a basis set, since the core region is probably insufficiently flexible for rigorous interpretation, but that's not a sin in my book. 3) UHF suffers from "overpolarization" from spin contamination (if that contamination is severe, the MP2 densities are not very useful either). ROHF, on the other hand, gives a nice first order spin density, but obviously contains no polarization at all of doubly filled orbitals. PUHF is a useful compromise, but still not as good as MP2 in most cases (and is not variational in the orbitals). Semiempirical results are awful, in my opinion, but that does not stop them from being reported on a large scale. If the system is too big to do higher levels of theory, the INDO approximation appears to have the most support. 4) DFT in our hands (pick a functional and we've probably tried it) is not much better than UHF for the same geometries, and is significantly worse for the many cases we have found where DFT is unable to reproduce the structure of the radical accurately (e.g., DFT predicts the experimentally observed PCl4 radical to be unstable to dissociation to PCl3 and Cl for several of the more modern functionals). The recent work of Salahub and Barone and Ishii and Shimizu provides other perspectives, but tends to keep me of the opinion that more work needs to be done in this area. Our paper on the phosphorus work was written with a very thorough introduction that addresses several of these points and is heavily referenced to the many outstanding contributions that others made to this field long before it attracted our interest. Rather than reproduce all those references here, I will simply point you to the article, Cramer and Lim J. Phys. Chem. 98 (1994) 5024-5033. As for other points you raised, isotropic hyperfine couplings may be calculated easily from the Fermi contact integral (the unpaired density at the nuclear position) which programs like Gaussian and I think AMPAC or MOPAC print out by default. The full hyperfine coupling tensor (of which the isotropic hyperfine coupling is the trace) is less trivial to come by. The code of Davidson and Feller called MELDF is quite useful--I am not immediately aware of other codes which accomplish this calculation in a canned way. The integrals for carrying it out are quite standard, and I believe many groups have simply hacked into whatever QM package they are using to add this capability. I note finally that several researchers use the approximation that hyperfine couplings can be calculated from the s orbital spin densities on individual atoms. We think this is a rather severe approximation that has never given good results in our hands, although experimentalists like it because it fits with the ways in which EPR spectra have traditionally been interpreted with repsect to "where" the unpaired electron is. Hope this is helpful! Chris -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 cramer@maroon.tc.umn.edu ----------------------- Me again from the answers I got I concluded that it is possible to predict EPR from ab initio calculations. You know what you need to have a good spin density and other things related to the EPR. The problem is that for large systems this can be very expensive. I do not have experience about DFT but from what I have read I see sometimes you have good results. When DFT fails you do not know why it happens. I am studying the interaction of alkaly and alkaline earth atoms with MgO surface. I am using ab initio methods. I have got some structural data about the metal-surface interaction. This kind of system has been studied by EPR and I would like to know how good is the spin density given by my calculation and the spin density given by EPR. The infomation I have received has been (and will be) quite useful for me. I hope it will be useful for other people. I wish to express my gratitude to people who answered me. Jose Antonio Mejias Dep. Quimica Fisica. Univ. Sevilla Spain e-mail: jamejias@obelix.cica.es From psubram@texaco.com Tue Oct 4 13:17:24 1994 Received: from texaco.com for psubram@texaco.com by www.ccl.net (8.6.9/930601.1506) id MAA07048; Tue, 4 Oct 1994 12:39:13 -0400 Received: by texaco.com (4.1/SMI-4.1) id AA15167; Tue, 4 Oct 94 11:38:48 CDT Date: Tue, 4 Oct 94 11:38:48 CDT From: psubram@texaco.com (Palavo Subramanian) Message-Id: <9410041638.AA15167@texaco.com> To: chemistry@ccl.net Subject: Interaction Energy using MOPAC Hi, I am interested in calculating interaction energies between 2 octane molecules. I would like to use MOPAC. Could someone let me know as to how I should go about setting the calculation etc. ( I am assuming that this can be done using MOPAC!). Thanks for your time, P.S.Subramanian(Mani) psubram@texaco.com From matt@synthesis.chem.arizona.edu Tue Oct 4 13:21:13 1994 Received: from synthesis.chem.arizona.edu for matt@synthesis.chem.arizona.edu by www.ccl.net (8.6.9/930601.1506) id NAA09932; Tue, 4 Oct 1994 13:08:03 -0400 Received: by synthesis.chem.arizona.edu (5.65/DEC-Ultrix/4.3) id AA04228; Tue, 4 Oct 1994 10:07:31 -0700 Date: Tue, 4 Oct 1994 10:07:31 -0700 (MST) From: Matt Stahl To: chemistry@ccl.net Subject: basis sets Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings, I'm in the process of modeling the transition state of methyl lithium addition to a ketone using ab initio methods. I'm curious to know what the experts would choose as a basis set for this problem. More specifically, would polarization functions (*) or diffuse functions (+) be more important for the modeling of this system correctly. I guess the question comes down to how much anionic character the "methyl" of the methyl-lithium has. Can anyone help me out on this? Thanks, matt ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Mr. Matthew Stahl | Department of Chemistry | I'd rather be right half of the University of Arizona | time than half right all the Tucson, AZ 85721 | time. matt@synthesis.chem.arizona.edu | -Malcom S. Forbes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From ccl@probe.ac1.uni-duesseldorf.de Tue Oct 4 13:26:31 1994 Received: from probe.ac1.uni-duesseldorf.de for ccl@probe.ac1.uni-duesseldorf.de by www.ccl.net (8.6.9/930601.1506) id MAA07053; Tue, 4 Oct 1994 12:39:31 -0400 Received: by probe.ac1.uni-duesseldorf.de (5.61/1.34) id AA27614; Tue, 4 Oct 94 17:36:39 +0100 From: ccl@probe.ac1.uni-duesseldorf.de (Computational Chemistry List) Message-Id: <9410041636.AA27614@probe.ac1.uni-duesseldorf.de> Subject: qsar - summary To: chemistry@ccl.net (Theochem-Liste) Date: Tue, 4 Oct 1994 17:36:39 +0100 (MET) X-Mailer: ELM [version 2.4 PL2] Content-Type: text Content-Length: 10430 Hi netters! A couple of weeks ago I started an inquiry about PD (what means Public Domain, 8-)) and non-PD software. Now I will summarize the received answers (as promised). Thanks to everybody, who helped me. My original question: ---------------------------------------------------------------------- Hi netters! I am searching for a program (PD preferred, but not absolutely necessary) for QSAR analysis (PC or SGI INDY with IRIX 5.2). I also need a little help in exploring the method, that means information about books and articles for beginners. I hope, I am not boring you with a question discussed often before. I looked for 'QSAR software' in the osc index files of 91-93 and didn't find much, so I think, I can run the risk of asking this question 8-) Naturally I will post a summary if desired. Thanks in advance Kay Kreidler ---------------------------------------------------------------------- An now the answers: [my comments in brackets]. ---------------------------------------------------------------------- To: Kay Kreidler Re: QSAR software If you would be kind enough to send me your address, I will have someone send you our literature on the QSAR software that we can provide within our Cerius2 environment. [I suppose, my .signature wasn't working. So I apologize for the missing information.] Along with an extremely easy to learn/use user interface, our QSAR functionality supports a variety of linear regression techniques (simple, stepwise, PLS) in addition to a novel genetic algorithm techniques that can provide a family of QSAR equations that can be non-linear. Cerius2 supports 46 descriptors "out of the box", and users are able to add new descriptors as their work requires. Descriptors can also be derived from a pseudo-receptor model for the active site. I look forward to hearing from you. [I received the information from Karen Faulkner of MSI] ------ Scott D. Kahn, Molecular Simulations Inc. (408) 522-0100 Email : scott@biocad.com; FAX (408) 522-0199 ---------------------------------------------------------------------- I would really like to receive information about your request. QSAR on IRIX 5.2. Yours truly, Ramiro Arratia-Perez Facultad de Quimica Pontificia Universidad Catolica de Chile [RAPEREZ@tacora.puc.cl] ---------------------------------------------------------------------- Kay: Would you please post a summary of PD QSAR software? I would appreciat it. John. John J. Isbell Department of Chemistry University of Texas at Austin Voice: (512) 471-0041 Austin, Texas 78751 Fax: (512) 471-8696 Email: cmkd344@utxvms.cc.utexas.edu ---------------------------------------------------------------------- The Sybyl modelling package has this built in, together with their excellent CoMFA method for 3D-QSAR. Runs on SGI machines. Contact Heather@tripos.com. Cheers, Dave [I tried to contact this address, but there was no response until today. Any suggestions?] __________________________________________________________________________ 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" ---------------------------------------------------------------------- First of all I'm not aware of any public domain (PD) software for QSAR, unless you count "pieces" like PD stat packages. The only software that I'm aware of that is specific for QSAR for the PC is a program called QSAR-PC from Biosoft. It has some rudimentary regression routines coupled to a substituent property database that can be used to assemble data tables. It is menu driven and will do Hansch and/or Free-Wilson analyses. This program is fairly affordable, ~US$199 but not as comprehensive as some of the others below, (the others below are also *much* more expensive $$$). Contact: Biosoft, PO Box 580, Milltown, NJ 08850 201/613-9013 or Biosoft, 22 Hills Road, Cambridge CB2 1JP, UK 0223 68622 For the SGI there is the QSAR module in Sybyl which performs Comparative Molecular Field Analysis, (CoMFA) but doesn't handle more traditional QSAR without having to piece together data sets from somewhere else. It does have tools for PLS, PCA & Cluster Analysis, but few property calc's and no substituent property database. Contact: Tripos Assoc., 1699 Hanley Rd., St. Louis, MO 63144 USA phone: 314-647-1099 There is a QSAR program from Oxford Molecular for the SGI that is specifically aimed at QSAR from several viewpoints called TSAR. This is the most complete QSAR package I have seen for specifically addressing QSAR. It has substituent methods and property databases as well as means to calculate a bunch of properties useful for QSAR. TSAR has a large number of statistical treatments and graphical means all in one place, which makes it quite valuable. Neural nets are being added and it can read files from other modeling pkgs. Contact: Oxford Molecular, 7005 Backlick Ct, Suite 200, Springfield, VA 22151 phone: 703-658-4854 As for fundamental literature to get started I would take a look at a few of these... [ Books ] "QSAR: Hansch Analysis and Related Approaches", Hugo Kubinyi, VCH, NY, 1993. (very good references) "Quantitative Drug Design - A Critical Introduction", Y. Martin, Marcel-Dekker, NY 1978. (also very good for fundamentals, however it is out-of-print,) (but your library may be able to get it through inter-library loan.) [ Papers ] C. Hansch and T. Fujita, JACS, 86, (1964), 1616. -| |-classics J. Topliss and R. Edwards, J. Med. Chem., 22, (1979), 1238. -| C. Hansch, Acc. Chem. Res., 26, (1993), 147. -| | J. Topliss, Perspect. in Drug Dis. and Des., 1, (1993), 253. |-good overviews | S. Wold, QSAR, 10, (1991), 191. -| Hope this helps to get you started! Regards, Greg +-----------------------------------------------------------------------+ | Gregory L. Durst Computational Chemistry | | phone: 317/337-3413 DowElanco R&D | | email: gdurst@dowelanco.com 9330 Zionsville Rd. Bldg 306/D2 | | Indianapolis, IN 46268 USA | +-----------------------------------------------------------------------+ ---------------------------------------------------------------------- Kay, A nice program for QSAR is distributed by Oxford Molecular it is called Tsar. Other than that I would recommend take any package of statistics that would let you perform multivariate analysis and fed it your own properties. REFERENCES: C Hansch and TE Klein Acc Chem Res 19:392(1986) T Fujita In Comprehensive Medicinal Chemistry Vol. 4, Pergamonm 1990. H Kubinyi same as above. LH Hall and LB Kier Reviews in Computational Chemistry Vol1, VCH, pp 367-422. R. Franke, Theoretical Drug Design Methods, Akademie Verlag, 1984. If you were thinking of 3D QSAR, RD Cramer etr al. JACS 110:5959 (1988) GR Marshall& RD Cramer, Trends in Pharm. Sci. 9: 285 (1988) Then you should contact TRIPOS Assoc. They are the ones that sell COMFA, the typical 3D QSAR program. Regards, Hugo O. Villar. Terrapin Technologies, Inc. 750-H Gateway Blvd. So. San Francisco, CA 94080. Phone (415) 244-9303. Fax (415) 244-9388 [hugo@montara.molres.org] ---------------------------------------------------------------------- If you can find a copy, read my 1978 book which others say was a real help to them getting started. Of course it is old...I am starting to revise it. Title is Quantitative Drug Design. Publisher is Marcel Dekker. As to software, there is quite a bit. I haven't used much of it because I am much more into molecular modeling... However, Oxford Molecular sells TSAR which looks pretty nice to me. I think the parameters are already in it. With Sybyl one can load in parameters or type them in and run sophisticated analyses from a molecular spreadsheet. Of course, it has the advantage that one can also do CoMFA 3D QSAR in the same context. @@@@@@@@@@@ Yvonne Martin, Senior Project Leader @ Computer Assisted Molecular Design Project @@@@@@@@ @ D-47E, AP9A-LL @ @ Abbott Laboratories @ @ One Abbott Park Road @@@@@@@@@@ Abbott Park, IL 60064 Phone: 708 937-5362 FAX: 708 937-2 [MARTIN@cmda.abbott.com] ---------------------------------------------------------------------- REGARDING QSAR Dear Kay, Your recent query to the CCL about QSAR software has been forwarded to me by a colleague. I hope that you don't mind getting replies from commercial companies! You may already be aware that the latest release of Cerius2 this month includes a suite of modules for Drug Discovery. This includes the C2 QSAR module, very straightforward and easy to use for generating quantitative structure-activity relationship models. Cerius2 also makes it very easy to use Molecular Shape Analysis, an extension of QSAR for generating quantitative measurements of molecular shape properties. The use of Genetic Algorithms to generate multiple QSAR models increases the likelihood that the best structure-activity relationships have been found. If I may, I will send an information pack by post. Do not hesitate to contact me if we can be of further assistance. Best regards Karen Faulkner ------------------------------------------------------- Karen Faulkner Academic Account Manager Molecular Simulations 240/250 The Quorum, Barnwell Road, Cambridge, CB5 8RE, England Telephone: + 44 223 413300 Fax: + 44 223 413301 email: kfaulkner@msicam.co.uk ------------------------------------------------------- That's all, folks. Again, thanks for your help. Now I have to make the decision, what to do... Unfortunately, it seems, that there is not enough money for such an expensive program. Kay Kreidler Department of Inorganic Chemistry Heinrich-Heine-University Duesseldorf Universitaetsstr. 1 40225 Duesseldorf Germany e-mail: kay@probe.ac1.uni-duesseldorf.de From upaep2@cca.pue.udlap.mx Tue Oct 4 14:17:24 1994 Received: from cca.pue.udlap.mx for upaep2@cca.pue.udlap.mx by www.ccl.net (8.6.9/930601.1506) id NAA12607; Tue, 4 Oct 1994 13:24:57 -0400 Received: by cca.pue.udlap.mx (4.1/SMI-4.0) id AA15195; Tue, 4 Oct 94 11:25:50 CST Date: Tue, 4 Oct 1994 11:24:28 -0600 (CST) From: "Mario Fco. Arce Martinez" Subject: Requesting info... To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi my name Jose Luis Guevara from Mexico, and I'm making an investigation for concluding the studies in the University. I will appreciate if you could help me with the FTP site for ShareWare software where I could find software related with 'Chemical Kinetics Studies & Chemical Reactors Design'. Also I would like to know where to find information about Laboratory tests for Styrene & Polystyrene Syntesis. Thanks a lot. My e-mail address: upaep2@udlapvms.pue.udlap.mx From theochem@ctc.com Tue Oct 4 16:19:45 1994 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.9/930601.1506) id PAA03275; Tue, 4 Oct 1994 15:22:47 -0400 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA04975; Tue, 4 Oct 1994 15:22:23 -0400 Received: by pauling.ctc.com (931110.SGI/930416.SGI.AUTO) for @server1.ctc.com:chemistry@ccl.net id AA04650; Tue, 4 Oct 94 15:24:36 -0400 From: theochem@ctc.com (Douglas Smith) Message-Id: <9410041924.AA04650@pauling.ctc.com> Subject: Call for Papers (2nd notice) To: chemistry@ccl.net (Computational Chemistry List) Date: Tue, 4 Oct 1994 15:24:35 -0500 (EDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2394 2nd Notice: SYMPOSIUM ANNOUNCEMENT and Call for Papers Data Flow Programming and Visualization in Chemistry American Chemical Society Meeting Anaheim, CA April 2 - 7, 1995 Purpose: This symposium will focus on the use of data flow programming paradigms such as, but not limited to, AVS, Explorer, and Data Explorer for the rapid prototyping, development, and coding of tools used in computational chemistry, particularly for visualization. Presentations will include software development as well as applications. Sponsors: This symposium is jointly sponsored by the Computers in Chemistry Division of hte American Chemical Society and by the Molecular Graphics Society. The symposium will be part of the COMP division program at the Spring (April 2 - 7) 1995 meeting of the American Chemical Society in Anaheim, CA. Organizers: This symposium is organized by Dr. Douglas A. Smith of Concurrent Technologies Corporation, Dr. George Famini of ERDEC, U.S. Army, and Dr. Arthur Olson of the Scripps Institute. Publication of Proceedings: The sponsors have arranged to have papers based on the presentations published in a special issue of the Journal of Molecular Graphics. Interested parties should contact Dr. Smith using the information below as soon as possible. Abstracts of no more than 150 words should be supplied no later than October 20, 1994 on ACS abstract forms. You can obtain these forms by calling the ACS at 202-872-4396. -- Douglas A. Smith Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. +---------------------------------+---------------------------------+ | "The juvenile sea squirt wanders through the sea searching for | | a suitable rock or hunk of coral to cling to and make its home | | for life. For this task it has a rudimentary nervous system. | | When it finds its spot and takes root, it doesn't need its | | brain any more so it eats it. It's rather like getting tenure." | | --source unknown | +-------------------------------------------------------------------+ From RAPEREZ@tacora.puc.cl Tue Oct 4 16:48:00 1994 Received: from tacora for RAPEREZ@tacora.puc.cl by www.ccl.net (8.6.9/930601.1506) id PAA03894; Tue, 4 Oct 1994 15:26:27 -0400 Received: from tacora.puc.cl by tacora.puc.cl (PMDF #12315) id <01HHVT0BAKJ490NWPZ@tacora.puc.cl>; Tue, 4 Oct 1994 15:21 PDT Date: Tue, 4 Oct 1994 15:21 PDT From: RAMIRO Subject: Quantum Chemist in Chile.. To: chemistry@ccl.net Message-id: <01HHVT0BAKJ490NWPZ@tacora.puc.cl> X-Organization: Pontificia Universidad Católica de Chile X-VMS-To: IN%"chemistry@ccl.net" From: IN%"MAILER-DAEMON@ccl.net" "Mail Delivery Subsystem for chemistry" 4-OCT-1994 15:17:54.41 To: IN%"RAPEREZ@tacora.puc.cl" CC: Subj: Message rejected by chemistry@ccl.net Received: from www.ccl.net by tacora.puc.cl (PMDF #12315) id <01HHVSSNZQEO90NSTE@tacora.puc.cl>; Tue, 4 Oct 1994 15:15 PDT Received: for chemistry-request@ccl.net by www.ccl.net (8.6.9/930601.1506) id PAA02080; Tue, 4 Oct 1994 15:17:19 -0400 Date: Tue, 4 Oct 1994 15:17:19 -0400 From: Mail Delivery Subsystem for chemistry Subject: Message rejected by chemistry@ccl.net To: RAPEREZ@tacora.puc.cl Message-id: <199410041917.PAA02080@www.ccl.net> Due to large volume, messages posted to chemistry@ccl.net are required to have a Subject: field (up to 40 characters) describing the topic of the message. Your message did not have this field and WAS REJECTED. Please resubmit your message to chemistry@ccl.net with the proper Subject: field. If you do not know how to create this field, please contact your computer system administrator. If your system does not have this feature contact the coordinator of this list at chemistry-request@ccl.net@ccl.net Thank you for your cooperation and sorry for the restriction. Your original message follows. List Coordinator: chemistry-request@ccl.net@ccl.net ---- The original message received by chemistry@ccl.net ---- From RAPEREZ@tacora.puc.cl Tue Oct 4 15:17:15 1994 Received: from tacora for RAPEREZ@tacora.puc.cl by www.ccl.net (8.6.9/930601.1506) id OAA27711; Tue, 4 Oct 1994 14:51:34 -0400 Received: from tacora.puc.cl by tacora.puc.cl (PMDF #12315) id <01HHVRTD3WJ490NWPZ@tacora.puc.cl>; Tue, 4 Oct 1994 14:47 PDT Date: Tue, 4 Oct 1994 14:47 PDT From: RAMIRO To: chemistry@ccl.net Message-id: <01HHVRTD3WJ490NWPZ@tacora.puc.cl> X-Organization: Pontificia Universidad Católica de Chile X-VMS-To: IN%"chemistry@ccl.net" Santiago 4 October,1994 Dear Colleagues, this letter may shock you. Last Friday September 1 (16:30 hrs) the Personnel Officer (non-academic) send me a letter comunicating that the Pontificia Universidad Catolica de Chile decided to cancel my academic position. This measure satisfy the current workers law (it comes from the Pinochet regime) but violates the academic university regulations. This measure has produced a LARGE REPULSIVE EFFECT from the chilean communities. There will be many public declarations in the chilean newspapers because this type of measures never were applied even in the military regime, I received the letter Friday afternoon to be effective October 1st. They gave me only 6 hrs to leave the Pontificia Universidad Catolica. I never was accused of anything nor I never was on trial and I was never cited by any authority to deffend myself. Since this is a PRIVATE UNIVERSITY this can be done but still they violated the academic regulations. The University of Chile the same Friday night offered me a position and also the University of Concepcion. Most of the letters and public declarations are being sent to: Rector Juan de Dios Vial Pontificia Universidad Catolica Santiago, Chile FAX: (562)-222-5515 It will be very important that the International Comunity must know this and my chilean colleagues are writting letter to the RECTOR rejecting this treatment for an academic and scientist. My latest publications are: 1. R. Arratia-Perez J. Chem. Phys. 1991, 95, 7239 2. R. Arratia-Perez, Chem. Phys. Lett. 1993, 203,409 3. R. Arratia-Perez and L. Hernandez-Acevedo, THEOCHEM 1993,282,131. 4. R. Arratia-Perez, Chem. Phys. Lett. 1993, 213, 547. 5. J.P. Bravo-Vazquez and R. Arratia-Perez, J. Phys.Chem. 1994,98,5627 Thanking before hand the International Solidarity. Dr. Ramiro Arratia-Perez Ex-Associate Professor of Quantum Chemistry Pontificia Universidad Catolica de Chile Santiago, Chile. ----- End of the message ----- From theochem@ctc.com Tue Oct 4 17:17:17 1994 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.9/930601.1506) id QAA09329; Tue, 4 Oct 1994 16:59:02 -0400 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA08049; Tue, 4 Oct 1994 16:58:45 -0400 Received: by pauling.ctc.com (931110.SGI/930416.SGI.AUTO) for @server1.ctc.com:chemistry@ccl.net id AA04868; Tue, 4 Oct 94 17:01:03 -0400 From: theochem@ctc.com (Douglas Smith) Message-Id: <9410042101.AA04868@pauling.ctc.com> Subject: COMP Newsletter To: chemistry@ccl.net (Computational Chemistry List) Date: Tue, 4 Oct 1994 17:01:01 -0500 (EDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1476 The Fall/Winter edition of the COMP News, the official newsletter of the Computers in Chemistry Division of the ACS, is being prepared for publication. At this time, anyone who still would like to contribute an article or advertisement to this issue has two weeks left to do so. If you are interested, please contact me via email, fax or phone as soon as possible. Information about upcoming meetings, recently held meetings, new public domain software, or other industry news is welcome. Items do not have to relate only to computational chemistry - after all, the division is Computers in Chemistry. Doug -- Douglas A. Smith Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. +---------------------------------+---------------------------------+ | "The juvenile sea squirt wanders through the sea searching for | | a suitable rock or hunk of coral to cling to and make its home | | for life. For this task it has a rudimentary nervous system. | | When it finds its spot and takes root, it doesn't need its | | brain any more so it eats it. It's rather like getting tenure." | | --source unknown | +-------------------------------------------------------------------+ From tsaito@src.sony.co.jp Tue Oct 4 21:17:28 1994 Received: from ns.iij.ad.jp for tsaito@src.sony.co.jp by www.ccl.net (8.6.9/930601.1506) id VAA12771; Tue, 4 Oct 1994 21:10:24 -0400 Received: from sonyinet.sony.co.jp (sonyinet.sony.co.jp [202.24.32.17]) by ns.iij.ad.jp (8.6.9+2.4Wb/3.3Wb-NS) with SMTP id KAA28298 for ; Wed, 5 Oct 1994 10:10:20 +0900 Received: from sonygw.sony.co.jp by sonyinet.sony.co.jp (4.2/6.4JAIN-1.0) id AA03154; Wed, 5 Oct 94 10:10:18 JST Received: from srcgw2.src.sony.co.jp by sonygw.sony.co.jp (4.0/6.4J.6) id AA06815; Wed, 5 Oct 94 10:08:15 JST Received: from srcwsb.src.sony.co.jp by srcgw2.src.sony.co.jp (4.2/Sony4.2MX) id AA02658; Wed, 5 Oct 94 10:10:00 JST Received: from localhost by srcwsb.src.sony.co.jp (4.0/6.4J.6-slave1.0) id AA13231; Wed, 5 Oct 94 10:10:14 JST Message-Id: <9410050110.AA13231@srcwsb.src.sony.co.jp> To: chemistry@ccl.net Cc: tsaito@src.sony.co.jp Subject: Benchmark Date: Wed, 05 Oct 94 10:10:13 +0900 From: Takayuki SAITO Dear Netters, Does anyone know a benchmark result of machine performance using computer chemistry programs; Gaussian, MOPAC, and so on. Machines which I'm interested in are HP9000/7XX, CRAY, and so forth. Takayuki Saito Center for Computational Science, Research Center, SONY Corporation Yokohama, Japan