From rvn@genie.terra.co.il Wed Jan 24 02:51:41 1996 Received: from genie.terra.co.il for rvn@genie.terra.co.il by www.ccl.net (8.6.10/950822.1) id CAA28642; Wed, 24 Jan 1996 02:37:03 -0500 Received: (from rvn@localhost) by genie.terra.co.il (8.6.12/8.6.12) id HAA03628; Wed, 24 Jan 1996 07:35:01 GMT Date: Wed, 24 Jan 1996 09:35:01 +0200 (IST) From: Reuven Bakalash X-Sender: rvn@genie.terra.co.il To: List CCL Subject: Parallel Gaussian? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL-netters, Can anyone tell me what parallel machines are used to run Gaussian. Are there comparative benchmarks? Thanks, Reuven Bakalash rvn@genie.terra.co.il From Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de Wed Jan 24 05:51:44 1996 Received: from ixgate02.dfnrelay.d400.de for Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de by www.ccl.net (8.6.10/950822.1) id FAA00637; Wed, 24 Jan 1996 05:42:37 -0500 X400-Received: by mta d400relay in /PRMD=dfnrelay/ADMD=d400/C=de/; Relayed; Wed, 24 Jan 1996 11:40:13 +0100 X400-Received: by /PRMD=HOECHST-AG/ADMD=D400/C=DE/; Relayed; Wed, 24 Jan 1996 11:38:34 +0100 X400-Received: by /PRMD=HOECHST-AG-MSM/ADMD=DBP/C=DE/; Relayed; Wed, 24 Jan 1996 11:34:49 +0100 Date: Wed, 24 Jan 1996 11:34:49 +0100 X400-Originator: Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=hoechst-ag-msm/ADMD=dbp/C=de/;960124103449] X400-Content-Type: P2-1984 (2) Content-Identifier: CSI NC V3.0 From: "Schiffer, Heinz, Dr., WIA / SC" Message-ID: <0019B327.MAI*/S=Schiffer/OU=MSMWIA/O=HOECHST/PRMD=hoechst-ag/ADMD=dbp/C=de/@MHS> To: CCL (Receipt Notification Requested) (Non Receipt Notification Requested) Subject: Geometry optimization Shridar Gadre wants to know the performance of various methods for geometry optimization of molecules. There are some good references in the literature about this subject, but it seems to me, that these are not well known in the computational chemistry community ( e.g. by looking through the list of questions in the CCL ). Therefore I give the list of my favourite references : For general optimization methods : R. Fletcher Practical Methods of Optimization Vol. 1 : Unconstrained Optimization Vol. 2 : Constrained Optimization Wiley, New York 1981 Most algorithms of Fletcher's books can be found as FORTRAN programs in : William H. Press, Brian P. Flannery, Saul A. Teukolsky, William T. Vetterling Numerical Recipes. The Art of Scientific Computing Cambridge University Press 1986 ( The FORTRAN routines are available on diskettes ! ) For geometry optimization of molecules : P. Pulay Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules. I. Theory Mol. Phys. 17 (1969) 197-204 J. W. McIver Jr. and A. Komornicki Rapid Geometry Optimization for Semi-Empirical Molecular Orbital Methods Chem. Phys. Lett. 10 (1971) 303-306 Dieter Poppinger Geometry Optimization in ab Initio Molecular Orbital Theory Chem. Phys. Lett. 34 (1975) 332-336 Richard L. Hilderbrandt Application of Newton-Raphson Optimization Techniques in Molecular Mechanics Calculations Computers & Chemistry 1 (1977) 179-186 Peter Pulay, Geza Fogarasi, Frank Pang, and James E. Boggs Systematic ab Initio Gradient Calculation of Molecular Geometries, Force Constants, and Dipole Moment Derivatives J. Am. Chem. Soc. 101 (1979) 2550-2560 M. B. Smirnov The Use of Internal Coordinates in the Variable Metric Method of Molecular Geometry Optimization J. Mol. Structure 65 (1980) 163-168 Fernando Bernardi, Andrea Bottoni, Glaudo Tonachini A Comparative Analysis of Various Gradient Methods for Geometry Optimization at the ab Initio SCF-MO Level J. Mol. Structure 86 (1981) 123-129 H. Bernhard Schlegel Estimating the Hessian for gradient-type geometry optimizations Theoret. Chim. Acta 66 (1984) 333-340 Pal Csaszar and Peter Pulay Geometry Optimization by Direct Inversion in the Iterative Subspace J. Mol. Structure 114 (1984) 31-34 John D. Head and Michael C. Zerner A Broyden-Fletcher-Goldfarb-Shanno Optimization Procedure for Molecular Geometries Chem. Phys. Lett. 122 (1985) 264-270 H. Bernhard Schlegel Optimization of Equilibrium Geometries and Transition Structures Adv. Chem. Phys. 67 (1987) 249-286 John D. Head Partial Optimization of Large Molecules and Clusters J. Comput. Chem. 11 (1990) 67-75 John F. Stanton, David E. Bernholdt An Empirically Adjusted Newton-Raphson Algorithm for Finding Local Minima on Molecular Potential Energy Surfaces J. Comput. Chem. 11 (1990) 58-63 Da-hong Lu, Meishan Zhao, and Donald G. Truhlar Projection Operator Method for Geometry Optimization with Constraints J. Comput. Chem. 12 (1991) 376-384 Peter Pulay, Geza Fogarasi, Xuefeng Zhou and Patterson W. Taylor Ab initio prediction of vibrational spectra : a database approach Vibrational Spectroscopy 1 (1990) 159-165 Jon Baker and Warren J. Hehre Geometry Optimization in Cartesian Coordinates : The End of the Z-Matrix ? J. Comput. Chem. 12 (1991) 606-610 Jon Baker Geometry Optimization in Cartesian Coordinates : Constrained Optimization J. Comput. Chem. 13 (1992) 240-253 Geza Fogarasi, Xuefeng Zhou, Patterson W. Taylor, and Peter Pulay The Calculation of ab Initio Molecular Geometries : Efficient Optimization by Natural Internal Coordinates and Empirical Correction by Offset Forces J. Am. Chem. Soc. 114 (1992) 8191-8201 P. Pulay and G. Fogarasi Geometry optimization in redundant internal coordinates J. Chem. Phys. 96 (1992) 2856-2860 Thomas H. Fischer and Jan Almloef General Methods for Geometry and Wave Function Optimization J. Phys. Chem. 96 (1992) 9768-9774 S. Vogel, T. H. Fischer, J. Hutter, and H. P. Luethi Third-Order Methods for Molecular Geometry Optimizations Int. J. Qunatum Chem. 45 (1993) 679-688 Jon Baker Techniques for Geometry Optimization : A Comparison of Cartesian and Natural Internal Coordinates J. Comput. Chem. 14 (1993) 1085-1100 Jon Baker and Doreen Bergeron Constrained Optimization in Cartesian Coordinates J. Comput. Chem. 14 (1993) 1339-1346 Chunyang Peng, Philippe Y. Ayala, H. Bernhard Schlegel, Michael J. Frisch Using redundant Internal Coordinates to Optimize Equilibrium Geometries and Transition States J. Comput. Chem. 17 (1996) 49-56 Roland Lindh, Anders Bernhardsson, Gunnar Karlstroem , Per-Ake Malmqvist On the use of a Hessian model function in molecular geometry optimizations Chem. Phys. Lett. 241 (1995) 423-428 Multiple Minima Problem : Martin Saunders, K. N. Houk, Yun-Dong Wu, W. Clark Still, Mark Lipton, George Chang and Wayne C. Guida Conformations of Cycloheptadecane. A Comparison of Methods for Conformational Searching J. Am. Chem. Soc. 112 (1990) 1419-1427 Costas D. Maranas and Christodoulos A. Floudas A deterministic global optimization approach for molecular structure determination J. Chem. Phys. 100 (1994) 1247-1261 Jordi Mestres and Gustavo E. Scuseria Genetic Algorithms : A Robust Scheme for Geometry Optimizations and Global Minimum Structure Problems J. Comput. Chem. 16 (1995) 729-742 Djurdje Cvijovic and Jacek Klinowski Taboo Search : An Approach to the Multiple Minima Problem Science 267 (1995) 664-666 Martin J. Field Global optimization using ab initio quantum mechanical potentials and simulated annealing of the classical Liouville equation J. Chem. Phys. 103 (1995) 3621-3628 ---------------------------------------------------------------------------- -------------------------------------------- Dr. Heinz Schiffer Phone : ++49-69-305-2330 Hoechst AG Fax : ++49-69-305-81162 Scientific Computing Email : schiffer@wia.hoechst-ag.d400.de 65926 Frankfurt am Main ---------------------------------------------------------------------------- --------------------------------------------- From owner-chemistry@ccl.net Wed Jan 24 10:06:47 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA04169; Wed, 24 Jan 1996 09:58:56 -0500 Received: from latina.chem.cinvestav.mx for antunez@chem.cinvestav.mx by bedrock.ccl.net (8.7.1/950822.1) id JAA25756; Wed, 24 Jan 1996 09:58:33 -0500 (EST) Received: by latina.chem.cinvestav.mx (5.x/SMI-SVR4) id AA22141; Wed, 24 Jan 1996 08:59:34 -0600 Date: Wed, 24 Jan 1996 08:59:33 -0600 (CST) From: Sandra Antunez To: chemistry@ccl.net Cc: antunez@chem.cinvestav.mx Subject: Latinamerican Chemistry Net Announcement Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE Dear Netters: I would like to announce that the Latinamerican Chemistry Net Site is now available at http://latina.chem.cinvestav.mx. While there is already useful information present, we hope to expand our offerings in the near future. Any suggestions and comments are welcome. In particular, we would like to hear from developers of academic, shareware, and freeware chemistry software for inclusion in our ftp site: latina.chem.cinvestav.mx.=20 Regards, Sandra Ant=FAnez Webmaster antunez@chem.cinvestav.mx Departamento de Qu=EDmica Centro de Investigaci=F3n y de Estudios Avanzados del I.P.N. MEXICO From pitsel@chemul.uni.lodz.pl Wed Jan 24 11:13:08 1996 Received: from chemul.uni.lodz.pl for pitsel@chemul.uni.lodz.pl by www.ccl.net (8.6.10/950822.1) id KAA06281; Wed, 24 Jan 1996 10:53:50 -0500 Received: by chemul.uni.lodz.pl (5.65/25-eef) id AA13025; Wed, 24 Jan 96 16:57:51 +0100 Message-Id: <9601241557.AA13025@chemul.uni.lodz.pl> From: pitsel@chemul.uni.lodz.pl (Piotr Seliger) X-Mailer: SCO System V Mail (version 3.2) To: chemistry@www.ccl.net Subject: Fe-NO bonding Date: Wed, 24 Jan 96 16:57:50 MEZ Hi netters, i am searching for some quantum chemistry results on Fe( Fe(+2)---N=O system as well as some geometry data on this molecule ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Piotr Seliger PPP I TTT SSS EEE L Department of General P P I T S E L and Inorganic Chemistry, PPP I T SSS EE L University of Lodz, P I T S E L Narutowicza 68, P I T SSS EEE LLL 90-136 Lodz, POLAND E-mail: pitsel@chemul.uni.lodz.pl "The right to knowledge is like or pitsel@krysia.uni.lodz.pl the right to life" (G.B.Shaw) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Wed Jan 24 11:51:48 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA07409; Wed, 24 Jan 1996 11:47:32 -0500 Received: from xr1.atlas.fr for Jean-Dominique.J.D.GUITTON@VITRY.RPR/RD/CRVA/BIOTECH.RP-RORER.rp.fr by bedrock.ccl.net (8.7.1/950822.1) id LAA27413; Wed, 24 Jan 1996 11:47:22 -0500 (EST) From: X400-Received: by /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Wed, 24 Jan 1996 17:46:19 +0100 X400-Received: by mta xr1.atlas.fr in /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Wed, 24 Jan 1996 17:46:19 +0100 X400-Received: by /ADMD=ATLAS/C=FR/; Relayed; Wed, 24 Jan 1996 17:46:14 +0100 X400-Received: by /PRMD=RP/ADMD=ATLAS/C=FR/; Relayed; Wed, 24 Jan 1996 18:19:32 +0100 Date: Wed, 24 Jan 1996 18:19:32 +0100 X400-Originator: Jean-Dominique.J.D.GUITTON@VITRY.RPR/RD/CRVA/BIOTECH.RP-RORER.rp.fr X400-Recipients: chemistry@ccl.net X400-MTS-Identifier: [/PRMD=RP/ADMD=ATLAS/C=FR/;SSWA 960124171928789911] X400-Content-Type: P2-1984 (2) Content-Identifier: chemical mixture Message-ID: <"SSWA 960124171928789911*/I=JD/G=Jean-Dominique/S=GUITTON/OU=VITRY/OU=RPR$/RD$/CRVA$/BIOTECH/O=RP-RORER/PRMD=RP/ADMD=ATLAS/C=FR/"@MHS> To: "X400 -CHEMIOSC *?:CHEMISTRY" Subject: chemical mixture safety Dear Netters does anybody knows something about the use of the buffer sodium cacodylate mixed with DTT? Is it dangerous? My own and recent experience is that it leads to the emission of a vapour with a very bad odor. Thank you in advance. Jean Dominique Guitton Rhone Poulenc Rorer jean-dominique.guitton@rp.fr From hey@mail2.nmri.nnmc.navy.mil Tue Jan 23 13:49:11 1996 Received: from mail2.nmri.nnmc.navy.mil for hey@mail2.nmri.nnmc.navy.mil by www.ccl.net (8.6.10/950822.1) id NAA16090; Tue, 23 Jan 1996 13:49:08 -0500 Received: from transfusion.nmri.nnmc.navy.mil ([131.158.70.224]) by mail2.nmri.nnmc.navy.mil with SMTP; Tue, 23 Jan 1996 13:49:15 -0500 (EST) Date: Tue, 23 Jan 1996 13:49:08 -0500 Message-Id: <199601231849.NAA16090@www.ccl.net> To: chemistry@www.ccl.net From: Jeff Hey Subject: AMBER bending parameters Dear fellow-CCL subscribers, I would like to do some molecular modeling of sugars using AMBER using Hyperchem. However, the parameters sets that I have available to me (AMBER2, AMBER3 and AMBERS) do not include bending parameters for the atom sequence O(S)-C(T)-OH (ie an ether oxygen bound to a sp3 carbon which has a hydroxyl group on it). Can anyone provide me with the values for the bending force constant (KTheta) and equilibrium bond angle (Theta eq) and/or a reference where I might be able to find these values for the AMBER force-field? (I realize that AMBER was created primarily for studies of proteins and nucleic acids, but even nucleic acids contain sugars!) thanks for taking the time to read this, best regards, Jeff ******************************************************************* Dr Jeff Hey Transfusion and Cryopreservation Research Program NMRI, Building 29, Naval Medical Centre, Bethesda, Maryland, 20889-5607. Telephone: (301) 295 6380 FAX: (301) 295 6083 E-mail: hey@mail2.nmri.nnmc.navy.mil ******************************************************************* From gl@coil.mdy.univie.ac.at Wed Jan 24 10:23:50 1996 Received: from coil.mdy.univie.ac.at for gl@coil.mdy.univie.ac.at by www.ccl.net (8.6.10/950822.1) id KAA04816; Wed, 24 Jan 1996 10:22:35 -0500 Received: by coil.mdy.univie.ac.at (940816.SGI.8.6.9/930416.SGI.AUTO) for chemistry@www.ccl.net id QAA00758; Wed, 24 Jan 1996 16:21:13 +0100 From: "Gerald Loeffler" Message-Id: <9601241621.ZM756@coil.mdy.univie.ac.at> Date: Wed, 24 Jan 1996 16:21:11 +0100 To: chemistry@www.ccl.net Subject: "Readable" DFT-code? Dear Computational Chemist! I would highly appreciate any help regarding the following: I'm looking for an "understandable", "good" (in the sense of good functionality as well as good from a software engineering standpoint) DFT-code, that is available at the usual inter-academic costs. The programming language it is written in is of no importance. The reason for that is, that I would like to have a DFT-program that I can experiment with and alter by incorporating new algorithms, removing unneeded functionality, selectively moving portions of it to a Molecular Mechanics code and heaven knows what else. To that end the code needs to be as compact as possible (no historic trash), clearly written and designed and maybe even commented (am I asking too much?). If you know such a DFT-code, I would be most grateful to hear from you! Yours, Gerald -- Gerald Loeffler PhD student in Theoretical Biochemistry EMail: Gerald.Loeffler@mdy.univie.ac.at Phone: +43 1 40480 612 Fax: +43 1 4028525 SMail: University of Vienna Institute for Theoretical Chemistry Theoretical Biochemistry Group Waehringerstrasse 17/Parterre A-1090 Wien, Austria From hey@mail2.nmri.nnmc.navy.mil Tue Jan 23 13:57:41 1996 Received: from mail2.nmri.nnmc.navy.mil for hey@mail2.nmri.nnmc.navy.mil by www.ccl.net (8.6.10/950822.1) id NAA16257; Tue, 23 Jan 1996 13:57:39 -0500 Date: Tue, 23 Jan 1996 13:57:39 -0500 Message-Id: <199601231857.NAA16257@www.ccl.net> Received: from transfusion.nmri.nnmc.navy.mil ([131.158.70.224]) by mail2.nmri.nnmc.navy.mil with SMTP; Tue, 23 Jan 1996 13:57:33 -0500 (EST) To: chemistry@www.ccl.net From: Jeff Hey Subject: Hydrogen disorder in ice crystals Dear fellow-CCL subscribers, I wish to create a computer model of an ice crystal that has hydrogen disorder and is therefore more "real" than a completely ordered ice lattice? Is anyone aware of a program that will enable me to reach this goal? thanks in advance, Jeff ******************************************************************* Dr Jeff Hey Transfusion and Cryopreservation Research Program NMRI, Building 29, Naval Medical Centre, Bethesda, Maryland, 20889-5607. Telephone: (301) 295 6380 FAX: (301) 295 6083 E-mail: hey@mail2.nmri.nnmc.navy.mil ******************************************************************* From amasunov@shiva.Hunter.CUNY.EDU Wed Jan 24 17:06:53 1996 Received: from hcrelay.hunter.cuny.edu for amasunov@shiva.Hunter.CUNY.EDU by www.ccl.net (8.6.10/950822.1) id RAA15687; Wed, 24 Jan 1996 17:03:06 -0500 Received: from shiva.hunter.cuny.edu (amasunov@shiva.hunter.cuny.edu [146.95.128.96]) by hcrelay.hunter.cuny.edu (8.6.12/george0995) with SMTP id RAA20751 for ; Wed, 24 Jan 1996 17:07:20 -0500 Date: Wed, 24 Jan 1996 17:03:46 -0500 (EST) From: Artem Masunov To: chemistry@www.ccl.net Subject: Dyes: Refs. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 24 Jan 1996, Ida N. L. Ma wrote: > Dear Dr. Masunov, > I am interested in calculations of dye properties. Can you point > me to some review of this topic, and references to your relevent > publications? > > yours sincerely, > Ida N. L. Ma > bcnlma@hkpv17.polyu.edu.hk Dear Dr. Ma, To the best of my knowlege, there is no review on this topic. Here are some referencies with comments in chaotic order: molecular mechanics calculations to predict ground state properties of 1,3,3,1',3',3'-hexamethylindoleninecarbocyanine: E. Akesson et al J. Chem. Phys. 95(9), 1 1991, page 6510 3,3'diethyl 2,2'oxacarbocyanine dyes J. Chem. Eng. Data, 1977, v. 22, n4, p.379 3,3'diethyl thiacarbocyanine dyes N.Tyutyulkov et al Polymethine Dyes. Structure and Properties. St Kliment Ohridsky University Press, Sofia 1991, p.132 3,3'-diethyl 2,2'thiacarbocyanine G. Ponterini, F. Momicchioli, Chem. Phys. 151 (1991) 111-126 X-ray P.J. Wheatley J.Chem.Soc. 1959, p.4096 K. Nakatsu et al Acta Cryst. 1977, B33, 2181 H. Yoshioka, K. Nakatsu,Chem. Phys. Lett. 1971, 11, 255 simple HMO prediction for quinolines D. A. Bahnick, J. Chem. Edu. 1994, 71, 171 NMR for 1,1'diethyl 2,2'pyridocyanine I. H. Leubner, Org. Magn. Resonance 1974, v.6, pp.253 [H2N-(CH)5=NH2+] ab initio SCF methods ref.18(French) in F.Momicchioli et al, Chem.Phys. 123 (1988) p.107bottom ab initio trimethyncyanine, pentamethyncyanine K. Schofel et al,Chem. Phys. Lett. 172 (1990) 187; T. Krossner F. Dietz, Chem. Phys. 153 (1991) 63-71 The rotational barriers are believed to be dramatically overestimated. ab initio H2N-CH=CH-CH=N(+)H2- (trimethincyanine) F. Momicchioli et. al, Spectrohim. Acta. 1990 46A, 5,775-791 excited state configurations F. Momicchioli et al, Chem. Phys. 123 (1988) 103-122, Ground state is-isomers of cyanines Rentsch S. Dietz F. Chem.Phys. 96 (1985) 145]: CNDO/S CI calcs. U. Dinur et al, Chem. Phys. Lett., 1980, 72, 3 , 493 "On the nature of excited electronic states in cyanine dyes:..." MNDO-CI calculations M.J.C. Dewar et al, J. Comput. Chem.,5, 480, 1984 SCF-CI calculations in p-electron approximation F. Dietz J. Signalaufz. Mater. 1981, 177 excited stste AM1 CI calculations in some dicarbocyanines M.M.Award, P.K.McCarthy, G.J.Blanchard et al., J. Phys. Chem. 1994, 98, 1454 (unrealistic peaks on potential curves) Not much, unfortunately that's it!!! Sincerely, AM __ _________ / \ / _ _ \ Artem Masunov - amasunov@shiva.hunter.cuny.edu / \\ \\ \\ \ Chemistry Department, Hunter College / /\ \\ \\ \\ \ City University of New York / ____ \\ \\ \\ \ 695 Park Avenue, New York, NY 10021 /__/\__/\__\\__\\__\\__\ Tel: (212) 725-0317, Fax: (212) 772-5332 \__\/ \/__//__//__//__/ I know you believe you understand what you think I said, but I am not sure you realize that what you heard is not what I meant. (Gaussian92)