From D.Winkler@chem.csiro.au Thu Mar 30 02:39:55 1995 Received: from auric.chem.csiro.au for D.Winkler@chem.csiro.au by www.ccl.net (8.6.10/930601.1506) id CAA11974; Thu, 30 Mar 1995 02:31:19 -0500 Received: from [138.194.40.149] (mac-40149.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA21269 (5.67b/IDA-1.5 for chemistry@ccl.net); Thu, 30 Mar 1995 17:28:23 +1000 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 30 Mar 1995 17:29:37 +1000 To: chminf-l@iubvm.ucs.indiana.edu, aschin-list@nuscc.nus.sg, chemistry@ccl.net, anchodd@tasman.cc.utas.edu.au From: D.Winkler@chem.csiro.au (Dr. Dave Winkler) Subject: Symposium at 6th Asian Chem Conf (Manila 22-25 May) Cc: b_duke@lacebark.ntu.edu.au, raj.godhia@cray.com As this is being posted to several lists I apologise for any duplication. C A L L F O R P A P E R S ONE DAY SYMPOSIUM ON COMPUTATIONAL CHEMISTRY AND MOLECULAR DESIGN at the 6th Asian Chemical Congress(6ACC) 22-25 May 1995 Phillipine Village Airport Hotel MANILLA, PHILLIPINES The symposium will cover research in computational chemistry, molecular design and bio-organic chemistry. The symposium will follow a similar format to that of the successful computational chemistry symposium held at the 5th Asian Chemical Congress in Kuala Lumpur in 1993. Papers discussing research conducted in any of these broad areas are now requested by the Symposium convenor. Further information on the 6ACC can be obtained from the 6ACC'95 Secretariat, c/o Phillipine Federation of Chemical Societies, U.P. NSRI Building, Diliman, Quezon City 1101, Phillipines Phone: 63-2-97-57-36 Fax: 63-2-99-68-68 63-2-97-57-74 63-2-819-3853 Email: chem@nicole.upd.edu.ph Requests for further information on the computational chemistry symposium, and expressions of interest, should be directed to the convenor:- Dr. David Winkler Phone: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Rosebank MDC Clayton 3168 Australia Abstracts of papers (one inch margins, A4 paper, single spaced 10 point Times, Courier, Pica or Elite typeface, title in bold capitals) should be submitted to the Secretariat as soon as possible. Please send copies to the computational chemistry convenor as well. P R O G R A M SESSION 1 0900-0930 Prof. Igor Novak (National University of Singapore) - "Experimental Theoretical Chemistry: A Contradiction in Terms?" 0930-1000 Dr. Xiao-Chuan Wang (Biosym Technologies)- "Pharmacophore Hypothesis Generation and 3D Database Search in the Discovery of Peptidomimetics: Endothelin Antagonists" 1000-1030 Contributed paper. 1030-1100 MORNING TEA SESSION 2 1100-1130 Dr. John Carpenter (Cray Research, USA) "Calculation of Structures and Interaction Energies of Mixed Hydrogen Bond Dimers by DFT and MP2 Methodology: How Accurate is DFT?" 1130-1200 Dr. Xiaoxia Li (LCC, Academia Sinica)- "Internet Network System and Resources for Chemistry- The Internet in China and WWW for ChIN" 1200-1230 Contributed paper. 1230-1400 LUNCH SESSION 3 1400-1430 Dr. Eiji Osawa (Toyohashi Institute, Japan)- "Conformations of C60 analogues" 1430-1500 Dr. Dave Winkler (CSIRO, Australia)- "Molecular orbital studies of conducting polymers" 1500-1530 Prof. Brian Duke (University of Northern Territory) "Aluminium and gallium hydrides and borohydrides - theory interacts with experiment" 1530-1600 AFTERNOON TEA SESSION 4 1600- Workshop on teaching of computational chemistry especially in the Asia/Pacific Area. Computational chemistry resources on the internet. This will be run by Prof. Brian Salter-Duke (University of Northern Territory) 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 CSIRO: http://www.csiro.au Private Bag 10,Rosebank MDC, Clayton, Australia From herbert.homeier@rchs1.chemie.uni-regensburg.de Thu Mar 30 03:24:57 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.10/930601.1506) id DAA12581; Thu, 30 Mar 1995 03:24:14 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA15111 (5.65c/IDA-1.4.4 for ); Thu, 30 Mar 1995 10:23:26 +0200 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA09407; Thu, 30 Mar 95 10:24:38 +0200 Date: Thu, 30 Mar 95 10:24:38 +0200 From: Herbert Homeier (t4720) Message-Id: <9503300824.AA09407@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Re: Complex Valued Hartree-Calculations Cc: AMFERREIRA@msuvx2.memphis.edu, aiba@ir.phys.chem.ethz.ch Dear netters, with regard to the following message I have some comments which are interspersed with the text of the message. > Mime-Version: 1.0 > X-Courtesy-Of: NCSA Mosaic 2.4 on Sun > X-Url: http://rchs1.chemie.uni-regensburg.de/%7Emaillist/data/1163.html > > CCL:Re: Complex Valued Hartree-Calculations > > Ayaz Bakasov, Phys. Chem., ETH Zurich (aiba@ir.phys.chem.ethz.ch) > Mon, 27 Mar 1995 23:51:56 +0200 > > Dear Netters, > > I think the question posted > by Antonio M. Ferreira > is a very interesting one. > Should I dare to pass this discission > on to our list ? > Here is his original question > and my (perhaps a bit hastily made) > reply. > Sincerely, > Ayaz Bakasov. > > > Date: 27-MAR-1995 22:22:28.46 > > From: ETHZ::""Antonio M. Ferreira" > > " > > Subj: Complex Valued Hartree-Calculations > > To: chem-comp@mailbase.ac.uk > > > > I am looking for any information concerning > > complex-valued HF calculatoins. I understand > > that this has been done in the past, however > > I have been unable to find the references. > > I would appreciate any information out there, > > particularly on such calculations using > > complex basis functions leading to complex > > density matricies. > > > >To anyone who can help me, I offer my appreciation > > and sincere thanks. > > > >Tony > > > > Dear Antonio M. Ferreira, > > I believe that the rejection of complex valued > SCF in quantum chemistry is a historical mistake > -- it will be eventually improved. > > The physical ground is that as long as > the main features of molecular behavour > are concerned, the Coulomb interaction > is the leading one - it strongly dominates > other interactions like spin-orbit or hyperfine. > The Coulomb interaction (taken solely) produces > a wave function which has a GLOBAL complex phase > which can be put equal to zero everywhere > in configuration space (at zero external fields). > > ONLY magnetic interactions lead > to the physical necessity to > compexify the wave function > and to introduce LOCAL complex phase > which depends on coordinates. > > For instance, in NMR it is a routine > to use complex wave functions > in ab initio calculations > though the magnetic fields are EXTERNAL. > Take as example the IGLO package. > > There are internal magnetic fields > but the bulk of quantum chemists > believe that they are not significant > for most of applications. > It is a prejudice and chemists > have no motivation to give it up yet. > And they make the weather in the field > -- the orthodox physicists left long time > ago for high energy physics, nuclear physics > and so forth (to look for "fundamental problems"), > so the molecular physics > was left to people who were really interested > in it - to chemists. :-) One comment here: The basic reason for using real wavefunctions/basis sets is probably the theorem that in a system with time reversal symmetry one can choose the wavefunction to be real IF spin is not considered. A similar statement including spin probably holds if closed shell systems are considered (if somebody has a proof or knows a reference, please send me an e-mail). However, there are certainly many systems (for instance open-shell systems) where complex MO's are necessary. > > So, "no need to use complex SCF" > for zero external magnetic fields. > > No reason to laugh - one has to have > more education in physics, and it will require > some time to overcome the > inertia to use MOSTLY real wave functions. > (stuff deleted) > I contacted MANY distinguished people > in computational molecular physics > or in "quantum chemistry" > (asking them this "silly" question). > It is a very firm consensus > NOT to use complex wave functions > - and no clear reason to that. > There are two more technical reasons for using real basis sets. Primo, the calculations with complex numbers are more time-comsuming than those with real ones, and they take a factor two more storage. Secundo, there are symmetry relations for the real orbitals that cut down the number of two-electron integrals to be computed (and/or stored). As a matter of fact, however, there are also (partly different) symmetry relations in the case of complex orbitals that can be used similarly IF only basis sets are used that contain for each function also its complex conjugate function. In this case, the number of two-electron integrals to be computed/stored can be reduced by the same factor as in the case of real AOs. However, the bookkeeping is somewhat more complicated (See p. 95ff in [1]). Certainly, one can still use real AO basis sets and allow for complex coefficients of the MOs. But then in the MO basis the above remark applies. [1] H. H. H. Homeier, Integraltransformationsmethoden und Quadraturverfahren f"ur Molek"ulintegrale mit B-Funktionen (Roderer, Regensburg, 1990) (in German). (stuff deleted) > Sincerely, > Ayaz Bakasov. > Greetings and best regards Herbert Homeier -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From gl@coil.mdy.univie.ac.at Thu Mar 30 03:39:56 1995 Received: from coil.mdy.univie.ac.at for gl@coil.mdy.univie.ac.at by www.ccl.net (8.6.10/930601.1506) id DAA12682; Thu, 30 Mar 1995 03:39:31 -0500 Received: by coil.mdy.univie.ac.at (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA24210; Thu, 30 Mar 95 10:38:59 +0200 From: "Gerald Loeffler" Message-Id: <9503301038.ZM24208@coil.mdy.univie.ac.at> Date: Thu, 30 Mar 1995 10:38:56 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: SUMMARY: Zn++ is coordinated by Cys- Mime-Version: 1.0 Encoding: 2 TEXT BOUNDARY, 64 MESSAGE, 2 TEXT BOUNDARY, 198 MESSAGE, 3 TEXT BOUNDARY Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.19503301038.ZM24208.mdy.univie.ac.at" -- --PART-BOUNDARY=.19503301038.ZM24208.mdy.univie.ac.at Encoding: 61 TEXT Content-Type: text/plain; charset=us-ascii Dear Net-Chemists, My question was: > Imagine Zn++ being coordinated by 3 Cys and 1 His in a Zinc Finger. > Do you think it is likely that the Cys looses its S-bound proton (at neutral > pH) because of the influence of the Zn++ ? > This would mean, that the Zn++ is coordinated by 3 (negative) Cys- and 1 > (neutral) His (the His holding a partial negative charge on one N). I got loads of useful responses. The CCL has indeed shown it's enourmous value! I'd like to thank Cameron Forde, Lars Hemmingssen, susan jackels, Ronald Knegtel, Lou Noodleman, Antonio Rosato, Ulf Ryde, P.Th. van Duijnen and Scot Wherland for contributing their knowledge. AND THE ANSWER IS: Cys is most certainly deprotonated when coordinating Zn++! Some people doubted whether all of the Cys residues would be deprotonated, but especially the calculations done by Ulf Ryde convinced me, that all three Cys residues are deprotonated (i.e. Cys-) when coordinated to Zn++ ! Some useful REFERENCES: 1) Andersson, P., Kvassman, J, Lindstroem, A., Olden, B. & Pettersson, G. (1981), Eur. J. Biochem. 113, 425-433 2) Kvassman, J., & Pettersson, G. (1979) Eur. J. Biochem. 100, 115-123 3) ccounts of Chemical Research, Vol. 28, p. 14, 1995, by J. M. Berg 4) Int. J. Quant. Chem. 52(1994)1229 5) Eur. Biophys. J., submitted by Ulf Ryde 6) Int.J.Quantum Chem. (1980) 17 651, J.Mol.Biol. (1989) 206 101 7) Biophys.Chem (1992) 43 139 Please find appended the complete text of the responses I got. Yours enlightened, gerald -- Gerald Loeffler PhD student in Theoretical Biochemistry Email: gl@mdy.univie.ac.at Phone: +43 1 40480 612 Fax: +43 1 4028525 Mail: University of Vienna Institute for Theoretical Chemistry Theoretical Biochemistry Group Waehringerstrasse 17/Parterre A-1090 Wien, Austria #include "fancy_ASCII_picture" #include "funny_statement" #include "standard_disclaimer" --PART-BOUNDARY=.19503301038.ZM24208.mdy.univie.ac.at Encoding: 193 text X-Zm-Content-Name: summary Content-Description: plain text Content-Type: text/plain ; charset=us-ascii -------------------------------------------------------------------------------- From: Cameron Forde Hello, In response to your posting about cysteine coordination to zinc in zinc fingers. In all cases that I know of the sulfur is deprotonated when coordinated to a metal atom. The pKa of a metal bound thiol increases by about six to eight (I guess that should be decreases, becomes more acidic) on coordination. This is true for alcohol or water as well. If cysteine starts with a pKa of 8.5 you would predict the pKa of the metal bound form to be 0.5 - 2.5. In aqueous media at neutral pH the proton would not reside long at the sulfur. If you would like I could hunt up some references that discuss this phenomenon. Good luck Cameron Forde cforde@alchemy.chem.utoronto.ca -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- From: teolas@garm.teokem.lu.se (Lars Hemmingssen) Hello Gerald ! Concerning your question on whether one of the cysteines in Zn-(Cys)3-His is pro tonated. In horse liver alcohol dehydrogenase you have a system which resembles the above mentioned somewhat: Zn-(Cys)2-His-H2O. I.e. one of the cysteines replaced with water - so to speak, and with this set of ligands, the pKa of the water is about 9.2 (Andersson, P., Kvassman, J, Lindstroem, A., Olden, B. & Pettersson, G. (1981), Eur. J. Biochem. 113, 425-433 and Kvassman, J., & Pettersson, G. (1979) Eur. J. Biochem. 100, 115-123.), quite a bit lowered as compared to free water (15.7). So I believe that none of the cysteines are protonated. Hoping that this may be usefull Yours Lars Hemmingsen -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- From: susan jackels Hi, Take a look at the article in Accounts of Chemical Research, Vol. 28, p. 14, 1995, by J. M. Berg. He claims that the cysteinate groups are deprotonated and make hydrogen bonds to nearby peptide amide hydrogens. I haven't reread the article carefully to find out if he mentions the charge on the complexes. Good Luck, Susan C. Jackels Department of Chemistry Wake Forest University Winston-Salem, NC 27109 Phone: (910)759-5514 FAX: (910)759-4656 Internet: sjackels@ac.wfu.edu -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- From: ronald@chem.rug.nl (Ronald Knegtel) Dear Gerald, concerning your question on zinc fingers: > > Imagine Zn++ being coordinated by 3 Cys and 1 His in a Zinc Finger. > Do you think it is likely that the Cys looses its S-bound proton (at neutral > pH) because of the influence of the Zn++ ? > This would mean, that the Zn++ is coordinated by 3 (negative) Cys- and 1 > (neutral) His (the His holding a partial negative charge on one N). Yes, I think the Cys is deprotonated. It functions similar as carboxyl groups liganding metals. When you would lower the pH of a zinc finger protein solution it would very easily denature because the Cys residues become protonated and the metal binding is lost (I did this several times during my PhD, not funny! ;->). I'm not sure about the charge, it could also be that during the folding of the protein somehow the Cys's sulphur atoms lose both a proton and an electron, rendering a net charge of +2 from the Zn ion. In fact, I feel this is more likely since many zinc fingers bind DNA and a net charge of -2 for a C4 zinc finger would be unfavourable for binding to negatively charged DNA, while a charge of +2 would be quite helpful. I hope this helps... Ronald Knegtel -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- From: lou@scripps.edu (Lou Noodleman) Gerald, I would consider that it is almost certain that it is Cys(-) (deprotonated) just as in FeS proteins. Lou Noodleman Molecular Biology, MB1 The Scripps Research Institute La Jolla, CA 92037, USA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- From: antonio@risc1.lrm.fi.cnr.it I am not very skilled in zinc fingers. But I now that in rubredoxins, which are electron transfer proteins, you have a Fe++ ion coordinated by four CYS all having lost their S proton. I hope this helps. Best wishes Antonio Rosato -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- From: teoulf@garm.teokem.lu.se (Ulf Ryde) Hi! In alcohol dehydrogenase there are two zinc(II) ions (in each subunit). The catalytic one is coordinated to two Cys, one His, and a water molecule. The structural zinc is coordinated to four Cys. It is usually assumed that all Cys ligands are deprotonated. For the catalytic zinc ion, the pKa of the zinc-bound water molecule is about 9.2, i.e. it is lowered by about 6.5 pKa units by the coordination to the zinc ion; therefore it seems very probable that a third Cys ligand would have a pKa well below 7 in the ZnCys3His complex. I have performed an extensive series of ab initio quantum chemical geometry optimisations on models of the catalytic zinc ion in alcohol dehydrogenase using SH- and CH3S- as a mimic of deprotonated Cys ligands, and the structures resemle the crystal structure very much (Int. J. Quant. Chem. 52(1994)1229). Yet, I did not actually try SH2 as a Cys model. Furthermore, I recently submitted a paper to Eur. Biophys. J., where I test the hypothesis that only two or three of the Cys ligands of the structural zinc ion are deprotonated (it was suggested by Garmer & Krauss in J. Am. Chem. Soc 114(1992)8191). I have optimised [Zn(SH)4]2-, [Zn(SH)3(SH2)]-, and [Zn(SH)2(SH2)2] with different ab initio methods and the results show that only [Zn(SH)4]2- can reproduce the Zn-S bond lengths found in the crystal structures. Thus, I think that you can safely assume that all three Cys ligands in the zinc fingers are deprotonated. Ulf Ryde Dep. Theoretical Chemistry University of Lund POB 124 S-221 00 Lund Sweden teoulf@garm.teokem.lu.se -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- From: ptvd@chem.rug.nl (van duijnen) Hi, It reminds me of the papain story [Int.J.Quantum Chem. (1980) 17 651, J.Mol.Biol. (1989) 206 101] in which Cys has a pK of about 4 and His of about 8! The paper rationalize this. Whether all three Cys residues and His become negative is doubtful. The negative charge on His will not be fully localized on N, and 'free' charges don't exist (counter ions, solvation, ...). But certainly the pKs will be influenced by the charge on Zn, in particular the pK of His which is extremely sensitive to the charge distribution of its direct environment. (See also Biophys.Chem (1992) 43 139) Good luck and keep me posted! Piet van Duijnen. P.Th. van Duijnen, Chemistry Department (OMAC), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands. tel. (int)-3150-634373 fax. (int)-3150-634296 e-mail: ptvd@chem.rug.nl -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- From: WHERLAND@WSUVM1.CSC.WSU.EDU Gerald Loeffler, A +2 metal ion will certainly shift the pKa of a ligand so that it will coordinate as the anion. The blue copper proteins and the iron sulfur proteins all have thiolate as a ligand. A neutral sulfur that cannot deprotonate, as in methionine sulfur, is a poor ligand. There is a significant discussion of the influence of the weak methionine ligand in the blue copper proteins. Data on the extent to which a metal ion can lower the pKa of an ionizable ligand are available. For example coordinated water is much more acidic, than bulk water. Bulk water pKa 14, Zn(2+)(aqueous) pKa 10.0. In this case the proton does remain on the water. Imidazole(protonated) pKa 7, imidazole coordinated to Cu(2+) pKa 3.8. In this case the proton is lost, since there is no pair of electrons to coordinate unless the proton is lost. Since sulfur could coordinate without deprotonating the possibility is there, but the pKa is low enough that it is likely to deprotonate, and there is extensive precedent. Scot Wherland Prof. of Chemistry Washington State Univ. -------------------------------------------------------------------------------- --PART-BOUNDARY=.19503301038.ZM24208.mdy.univie.ac.at-- From qftramos@usc.es Thu Mar 30 05:54:56 1995 Received: from uscmail.usc.es for qftramos@usc.es by www.ccl.net (8.6.10/930601.1506) id FAA13653; Thu, 30 Mar 1995 05:44:16 -0500 Received: by uscmail.usc.es (5.67b/1.34) id AA22428; Thu, 30 Mar 1995 12:47:21 +0200 Date: Thu, 30 Mar 1995 12:47:21 +0200 From: qftramos@usc.es (Antonio Fernandez Ramos) Message-Id: <199503301047.AA22428@uscmail.usc.es> To: chemistry@ccl.net Subject: second virial coef. Dear netters, Is any program available to calculate second virial coefficients if the intermolecular potential energy function of a poliatomic sistem is knew? From IB13LVIB@HUEARN.SZTAKI.HU Thu Mar 30 05:57:25 1995 Received: from phem3 for IB13LVIB@HUEARN.SZTAKI.HU by www.ccl.net (8.6.10/930601.1506) id FAA13648; Thu, 30 Mar 1995 05:43:50 -0500 Received: from HUEARN.SZTAKI.HU (MAILER@HUEARN) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HOQIEVKIY898POQE@phem3.acs.ohio-state.edu>; Thu, 30 Mar 1995 05:43:42 EST Received: from HUEARN (NJE origin IB13LVIB@HUEARN) by HUEARN.SZTAKI.HU (LMail V1.2a/1.8a) with BSMTP id 3391; Thu, 30 Mar 1995 12:42:53 +0200 Date: Thu, 30 Mar 1995 12:42:52 +0100 (CET) From: Istvan Mayer Subject: Ab initio bond orders To: CHEMISTRY@ccl.net Message-id: <01HOQIEX08GM98POQE@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT X-Acknowledge-To: Dear Netters, There was a question in CCL about ab initio bond orders. I shall to summarize here some points which I feel relevant in this respect. Among the programs I know, bond order analysis is CORRECTLY implemented in MONSTERGAUSS and HONDO-8 systems. (In HONDO-8 the term "bond index" is used.) It is implemented in GAMESS and Gaussian-92, too, but gives correct results only for CLOSED SHELL systems (except, perhaps, very fresh releases of GAMESS). In Gaussian-92 the bond orders are calculated as a part of the natural bonding orbital (NBO) analysis. The point is in the following. Bond orders and valences for ab initio wave functions were introduced in my paper I. Mayer, Chem. Phys. Letters 97, 270 (1983), but it became clear very soon that the definition given there for open shell systems must be modified because, e.g. the bond order for H2(+) ion was predicted 1/4 instead of the chemically expected 1/2. This modification was made in an Addendum to the paper mentioned [CPL 117, 396 (1985)], while the problem was discussed in detail in the paper Int. J. Quant. Chem. 29, 73 (1986) - where the generalization of bond orders and valences for correlated wave functions was also introduced. In GAMESS and Gaussian-92 the obsolete formulas of the first paper were implemented for open-shell systems. At the end of the last year I have prepared a revised routine for GAMESS which was then rewritten by the authors of the program in their style - so now they probably distribute this correct version. The only drawback is that due to some misunderstanding they have included a RETURN (with no bond order calculations) for GVB-type wave functions, although calculation for SINGLET GHF wave functions is also possible, using the same code. (May be this is also corrected in the meantime?) I have contacted also Gaussian Inc. with this problem, but they refused do deal with it in a somewhat arrogant manner - except promising that they will EXCLUDE open shell bond order calculations from their next, Gaussian-94 program. I am ready to help to those who are not afraid of doing some programming work by sending them my versions. With best regards to all CCL, Istvan Mayer Central Research Institute for Chemistry of the Hungarian Academy of Sciences E-mail: IB13lVIB@HUBPSZ12.sztaki.hu (or IB13lVIB@HUEARN.bitnet) (Reserve path: H1376May@ella.hu or H1376May@HUELLA.bitnet) From praa2@cluster1.urz.uni-halle.de Thu Mar 30 09:25:00 1995 Received: from mlucom.urz.uni-halle.de for praa2@cluster1.urz.uni-halle.de by www.ccl.net (8.6.10/930601.1506) id JAA15560; Thu, 30 Mar 1995 09:16:32 -0500 From: Received: from cluster1.urz.Uni-Halle.DE by mlucom.urz.uni-halle.de with SMTP (1.36.108.7/15.6) id AA07627; Thu, 30 Mar 1995 16:14:57 +0200 Posted-Date: Thu, 30 Mar 1995 16:14:00 +0200 (MESZ) Received-Date: Thu, 30 Mar 1995 16:14:57 +0200 Received: by cluster1.urz.uni-halle.de (AIX 3.2/UCB 5.64/4.03) id AA41977; Thu, 30 Mar 1995 16:14:00 +0200 Message-Id: <9503301414.AA41977@cluster1.urz.uni-halle.de> Subject: 'low cost' methods available ? To: chemistry@ccl.net Date: Thu, 30 Mar 1995 16:14:00 +0200 (MESZ) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 1312 Dear colleagues, I'm trying to model the key steps of catalytic reactions involving one or several transition metal atoms (for the present only 1st row TM atoms are involved). Because of the largeness of the systems ab-initio techniques (HF-, post-HF or DFT) can only be applied to distict pre-evaluted key structures (or simplfied models) wich are previously examined by any lower cost methods. Such methods are the common semiempirical approaches (CNDO, ZINDO, NDDO-type methods, ...) or maybe force field methods, but they should yield reliable enough results. Our experiences with ZINDO are not so encouranging because they not give the desired accuracy of the results. We are mainly interested in describing the interaction of saturated/unsaturated hydrocarbons with nickel. So there is my question. Are there any recommended 'low cost' methods available that can be used side by side with ab-initio techniques in order to get a basic knowledge of the potential energy surface, that can be used in further examinations by ab-initio methods ? Is there a way out to self-contruct an appropriate force field for nickel describing the structural and energetical behaviour of some model systems obtained by ab-initio methods ? Any hints, suggestions or pointers are highly appreciated. Regards Peter From aholder@CCTR.UMKC.EDU Thu Mar 30 09:39:59 1995 Received: from axp1.umkc.edu for aholder@CCTR.UMKC.EDU by www.ccl.net (8.6.10/930601.1506) id JAA15654; Thu, 30 Mar 1995 09:27:10 -0500 Received: by CCTR.UMKC.EDU (MX V4.1 AXP) id 302; Thu, 30 Mar 1995 08:27:03 CST Date: Thu, 30 Mar 1995 08:27:03 CST From: Andy Holder To: CHEMISTRY@ccl.net Message-ID: <0098E200.7FBB0936.302@CCTR.UMKC.EDU> Subject: ACS in Anaheim Netters, Semichem will be demonstrating our AMPAC 5.0 with Graphical User Interface software at the ACS meeting in Anaheim next week. Please feel free to stop by the DEC or IBM booth to take a look and discuss AMPAC's present and future capabilities with eith myself or Roy Dennington. Regards, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President, Semichem Semichem, Inc. || Internet Addr: aholder@cctr.umkc.edu 7128 Summit || Phone Number: (913) 268-3271 Shawnee, KS, 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | | | "Semichem, The AMPAC people." | | | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From aholder@CCTR.UMKC.EDU Thu Mar 30 09:43:54 1995 Received: from axp1.umkc.edu for aholder@CCTR.UMKC.EDU by www.ccl.net (8.6.10/930601.1506) id JAA15632; Thu, 30 Mar 1995 09:25:05 -0500 Received: by CCTR.UMKC.EDU (MX V4.1 AXP) id 131; Thu, 30 Mar 1995 08:25:03 CST Date: Thu, 30 Mar 1995 08:25:02 CST From: Andy Holder To: CHEMISTRY@ccl.net Message-ID: <0098E200.382650CB.131@CCTR.UMKC.EDU> Subject: Chemistry Software for DEC Alpha Hello Netters. I wanted to add our AMPAC 5.0 with Graphical User Interface to the list of software available for the DEC Alpha AXP under both OpenVMS and OSF/1. AMPAC is a complete semiempirical calculations package with a graphical interface running under X-Windows Motif for easy and seamless network access. Our interface also is compatible with Gaussian's ab initio software. Regards, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President, Semichem Semichem, Inc. || Internet Addr: aholder@cctr.umkc.edu 7128 Summit || Phone Number: (913) 268-3271 Shawnee, KS, 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | | | "Semichem, The AMPAC people." | | | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From zhy@pchsgi25.IPC.PKU.EDU.CN Thu Mar 30 10:10:02 1995 Received: from pchsgi25.IPC.PKU.EDU.CN for zhy@pchsgi25.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/930601.1506) id JAA16318; Thu, 30 Mar 1995 09:55:59 -0500 Received: by pchsgi25.IPC.PKU.EDU.CN (911016.SGI/911001.SGI) for CHEMISTRY@ccl.net id AA18908; Thu, 30 Mar 95 22:52:23 +0800 Date: Thu, 30 Mar 95 22:52:23 +0800 From: zhy@pchsgi25.IPC.PKU.EDU.CN (Zhang Hongyu) Message-Id: <9503301452.AA18908@pchsgi25.IPC.PKU.EDU.CN> To: CHEMISTRY@ccl.net Subject: Request of 3d graph software Dear Netters, I will be very pleased to learn from you where to get a good 3d graph software in PC or workstation, here I need to draw a 3d graph from a series of f(x,y) points. Thanks in advance. Henry H. Zhang ---------------------------------------------------------------------- Henry Hongyu Zhang, Ph.D. student | email: zhy@pchsgi25.ipc.pku.edu.cn Molecular Design Laboratory | Tel: 861-2501490 Institute of Physical Chemistry | Fax: 861-2501725 Peking University | Peking 100871 , China | ----------- Too stiff, easily broken Too soft, easily crashed ------------ old Chinese Saying From jim@volvo.wavefun.com Thu Mar 30 14:10:03 1995 Received: from volvo.wavefun.com for jim@volvo.wavefun.com by www.ccl.net (8.6.10/930601.1506) id OAA21407; Thu, 30 Mar 1995 14:08:59 -0500 Received: from acura.wavefun.com by volvo.wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA07472; Thu, 30 Mar 95 11:09:17 -0800 Received: from isuzu.wavefun.com by acura.wavefun.com via SMTP (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA28636; Thu, 30 Mar 95 11:09:03 -0800 Message-Id: <9503301909.AA28636@acura.wavefun.com> X-Sender: jim@acura.wavefun.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 30 Mar 1995 11:12:49 -0800 To: chemistry@ccl.net From: jim@volvo.wavefun.com (jim Parisi) Subject: Announcement: SPARTAN 4.0 Wavefunction's SPARTAN Version 4.0 is now available. Among many others, enhancements to SPARTAN, the modeling package combining computational methods (ab initio, density functional, semi-empirical, molecular mechanics) with exceptional visualization, include: 1. PM3 for transition metals. 2. Thiel's MNDO/d method. 3. Conformational Searching has been improved to include systematic, Monte Carlo and genetic algorithms, and an interface to DGEOM. 4. A module for molecule superposition and similarity analysis. 5. A Density Functional Module. 6. Isosurfaces may now be produced from graphical volume data allowing the value of the surface to be re-defined in real time. 7. A module for coordinate driving in one or several dimensions. 8 Lists of molecules may be constructed and processed. 9. Enhanced QSAR descriptors. For detailed information about SPARTAN 4.0, contact me directly, visit the SPARTAN web page at http://wavefun.com, or stop by the Wavefunction booth at the ACS Convention in Anaheim, Island Booth #1511 in Hall B. Thank You. Jim Parisi Marketing/Sales Coordinator _________________________________________________________________ WAVEFUNCTION, INC. Phone: 714-955-2120 18401 Von Karman, Suite 370 FAX: 714-955-2118 Irvine, CA e-mail: jim@wavefun.com 92715 USA WEB: http://wavefun.com ----------------------------------------------------------------- C A R P E D I E M _________________________________________________________________ From jim@volvo.wavefun.com Thu Mar 30 14:25:02 1995 Received: from volvo.wavefun.com for jim@volvo.wavefun.com by www.ccl.net (8.6.10/930601.1506) id OAA21559; Thu, 30 Mar 1995 14:15:17 -0500 Received: from acura.wavefun.com by volvo.wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA07482; Thu, 30 Mar 95 11:15:36 -0800 Received: from isuzu.wavefun.com by acura.wavefun.com via SMTP (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA28686; Thu, 30 Mar 95 11:15:22 -0800 Message-Id: <9503301915.AA28686@acura.wavefun.com> X-Sender: jim@acura.wavefun.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 30 Mar 1995 11:19:08 -0800 To: chemistry@ccl.net From: jim@volvo.wavefun.com (jim Parisi) Subject: Announcement: Hehre's "Practical Strategies..." "Practical Strategies for Electronic Structure Calculations" by Warren J. Hehre, PhD Wavefunction would also like to announce the release of Warren Hehre's "Practical Strategies for Electronic Structure Calculations". This book, developed out of a short course offered at Wavefunction, is intended to serve as a guide to the use of modern electronic structure calculations, including semi-empirical, ab initio, and density functional. Aimed at research chemists looking to apply computational techniques to real chemical problems, the book's focus is entirely on the practical aspects of performing calculations. Priced at $25, this book is available only through Wavefunction. For detailed information, please contact me directly, or just send your name, address, phone number and a purchase order number to Wavefunction, either by fax or e-mail. Thank You. Jim Parisi Marketing/Sales Coordinator _________________________________________________________________ WAVEFUNCTION, INC. Phone: 714-955-2120 18401 Von Karman, Suite 370 FAX: 714-955-2118 Irvine, CA e-mail: jim@wavefun.com 92715 USA WEB: http://wavefun.com ----------------------------------------------------------------- C A R P E D I E M _________________________________________________________________