From ccl@cric.chemres.hu Mon May 22 06:08:51 1995 Received: from cric.chemres.hu for ccl@cric.chemres.hu by www.ccl.net (8.6.10/930601.1506) id FAA16375; Mon, 22 May 1995 05:56:12 -0400 From: Received: by cric.chemres.hu (AIX 3.2/UCB 5.64/4.03) id AA19512; Mon, 22 May 1995 11:52:18 +0200 Date: Mon, 22 May 1995 11:52:18 +0200 (DFT) To: Garcia Edgardo Cc: chemistry@ccl.net Subject: Re: CCL:BSSE & DFT In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 19 May 1995, Garcia Edgardo wrote: > > There was some discusion on the net about DFT last week. > I have a more practical question about DFT that I hope > you can answer and/or point some literature. > > Is there any study on BSSE with DFT methods ? > Does it show BSSE ? > Is there any stablished method to evaluate BSSE ? > > Thanks for any comments on that. > > Edgardo Garcia > Cristol Chem & Biochem > Univ. of Colorado > BOULDER CO USA > Yes, BSSE does appear in the LCAO-type DFT calculations, too. Both a posteriori counterpoise correction (a la Boys & Bernardi) and a priori exclusion of BSSE by CHA (Chemical Hamiltonian Approach) are feasible. For reference see: M. Kieninger, S. Suhai and I. Mayer, Chem. Phys. Letters 230, 485 (1994) I. Mayer e-mail: mayer@cric.chemres.hu Central Research Institute for Chemistry of the Hungarian Academy of Sciences H-1525 Budapest, P.O.Box 17 Hungary From rvgloss@criba.edu.ar Mon May 22 08:38:54 1995 Received: from sic4.cnea.edu.ar for rvgloss@criba.edu.ar by www.ccl.net (8.6.10/930601.1506) id IAA18349; Mon, 22 May 1995 08:38:34 -0400 Received: from criba.edu.ar by sic4.cnea.edu.ar with smtp (Smail3.1.28.1 #1) id m0sDWjJ-00040CC; Mon, 22 May 95 09:37 GMT-3:00 Received: by criba.edu.ar (4.1/SMI-4.1) id AA25650; Sun, 21 May 95 22:13:50 WST Date: Sun, 21 May 95 22:13:50 WST From: rvgloss@criba.edu.ar (Daniel Glossman) Message-Id: <9505220213.AA25650@criba.edu.ar> To: chemistry@ccl.net Subject: food additives Dear netters: There has been recently several nice summaries on this net in relation with the successes of computational chemistry on the study of chemical reactivity and molecular design. It is possible to find similar summaries on the literature (i.e., chapter 10 in the volume 1 of the Reviews in Computational Chemistry, K.B. Lipkowitz and D.B. Boyd, eds). Notwithstanding, most of the examples are related with compounds of explicit biological activity, like pharmaceuticals, pesticides and so on. My question is: Can somebody point me to bibliography related with computational chemistry, QSAR or computed-aided molecular design of molecules that can be potentially used as food additives? Thanks in advance Daniel Glossman ************************************************************************ Dr. Daniel Glossman Universidad Nacional de Lujan Departamento de Ciencias Basicas Laboratorio de Quimica Teorica y Computacional Casilla de Correo 221 (6700) Lujan - Republica Argentina E-mail: rvgloss@arcriba.edu.ar glossman@unlu01.edu.ar From jkl@ccl.net Mon May 22 12:53:56 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.10/930601.1506) id MAA23340; Mon, 22 May 1995 12:44:31 -0400 Date: Mon, 22 May 1995 12:44:31 -0400 From: Jan Labanowski Message-Id: <199505221644.MAA23340@www.ccl.net> To: chemistry@ccl.net Subject: CONFERENCE ON THEORETICAL ASPECTS OF HETEROGENEOUS CATALYSIS Cc: jkl@ccl.net Author: ricart@argo.urv.es (Josep M. Ricart) at NOTE 6th INTERNATIONAL CONFERENCE ON THEORETICAL ASPECTS OF HETEROGENEOUS CATALYSIS >>>>>>>>>>>>>>>>>>>>>>>>>>> C A T - 9 6 <<<<<<<<<<<<<<<<<<<<<<<< TARRAGONA CATALONIA, SPAIN JUNE 2-7, 1996 ------------------ FIRST ANNOUNCEMENT ___________________________________________________ Dear Colleague: After the success of the five previous meetings, (Lyon, 1986; Zacopane, 1988; Berkeley, 1990; Krakow, 1992 and Berlin, 1994) we cordially invite you to participate in the 6th International Conference on Theoretical Aspects of Heterogeneous Catalysis, which will be held in Tarragona, Spain, 2-7 June 1996. Tarragona was founded by the Romans in about 218 B.C. Many monuments have been preserved from the time when it was the capital of the Hispania Citerior: praetorium, circus, amphitheatre, aqueduct, forum walls etc. Situated on the mediterranean coast, Tarragona is a fine, commercially active city of 110,000 inhabitants; it has pleasant avenues, a look-out point over the Mediterraneum and an archeological walk round the old city walls. It is easily accesible by air, rail or road. Barcelona airport is about 90 Km away and linked to Tarragona by numerous trains. The E-2 highway links Tarragona to the main routes in Spain and abroad. SCIENTIFIC PROGRAM The scientific program will include oral lectures and poster presentations; there will be both invited and, a few, contributed lectures. It is also planned to organize a roundtable discussion session. SCOPE There are two primary objectives for this meeting. The first is to report information about recent advances in the study and understanding of surface properties and processes relevant to catalysis. The second is to develop and strengthen interactions between theory and experiment. The major focus of the meeting will be on theory but there will be several experimental presentations which will help to establish connections between measured properties and theoretical interpretations. TOPICS Metals and/or metal oxides in catalytic systems. Theoretical concepts and computational methods. Reactions on surfaces and clusters. Acid-base catalysis. Thin films and supported clusters. Surface reaction dynamics. SCIENTIFIC COMMITTEE G. Ertl (Germany). D. King (England). R. van Santen (The Netherlands). H. Sellers (USA). V. Staemmler (Germany). INVITED SPEAKERS The following scientists have already agreed to present an invited lecture: M. Asensio (Spain). P. S. Bagus (USA). R. Dovesi (Italy). W. A. Goddard III (USA). D. W. Goodman (USA). O. Gropen (Norway). M. Grunze (Germany). K. Hermann (Germany). D. King (England). G. Pacchioni (Italy). F. Ruette (Venezuela). M. Salmeron (USA). J. Sauer (Germany). H. Sellers (USA). U. Wahlgren (Sweden). ORGANIZING COMMITTEE P. S. Bagus, U. Barcelona. R. Caballol, U. Rovira i Virgili. J. Casanovas, U. Rovira i Virgili. A. Clotet, U. Rovira i Virgili. F. Illas, U. Barcelona. A. Povill, U. Barcelona. J. M. Ricart, U. Rovira i Virgili. J. Rubio, U. Barcelona. C. Sousa, U. Barcelona. S. Zurita, U. Barcelona. PROCEEDINGS Selected papers will be published as a special issue of a scientific journal. REGISTRATION FEE The registration fee for active participants will be US$ 250. This includes a book of abstracts to be distributed at the meeting and a bound Conference Proceedings to be distributed as soon as possible after the Conference. The Conference Dinner, other social events, and the coffee breaks are also included. A small number of fellowships to cover the conference fees for students will be available. Please request information through the conference E-mail address. ACCOMODATION Accomodation may be reserved on the registration form which we will be distributed together with the Second announcement. ACCOMPANYING PERSONS A social program will be arranged for accompanying persons. No registration fee is required. SECOND ANNOUNCEMENT Second circular will be distributed around November 1995 to those who send the pre-registration form before September 30th 1995. UNDER THE AUSPICIES OF Universitat Rovira i Virgili. Universitat de Barcelona. Comissionat per a Universitats i Recerca - CIRIT DGYCIT Societat Catalana de Quimica. Grup de Quimica Teorica de Catalunya. INFORMATION Prof. Dr. F. Illas, Prof. Dr. J.M. Ricart, Dept. Quimica Fisica, Dept. Quimica, Universitat de Barcelona Universitat Rovira i Virgili C/ Marti i Franques, 1 P. Imperial Tarraco 08028 Barcelona 43005 Tarragona SPAIN SPAIN Phone: 34-3-4021229 Phone: 34-77-559568 Fax: 34-3-4021231 Fax: 34-77-559563 Conference e-mail:cat96@quimica.urv.es Please circulate this first announcement among your colleagues. ________________________________________________________________ ================================================================ PRELIMINARY REGISTRATION FORM Please fill out and return. Last name: First name: Organization: Department: Street address: City and code: Country: E-mail: Tel: Fax: I plan to participate : YES: ____ PROBABLY: _____ I would like to make a contribution: YES: ______ NO: ______ Preferred form for my contribution: POSTER: _____ ORAL _____ Tentative title: _______________________________________________________________________ Number of accompanying persons: ________ <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> From antonio@risc1.lrm.fi.cnr.it Mon May 22 14:24:06 1995 Received: from risc1.lrm.fi.cnr.it for antonio@risc1.lrm.fi.cnr.it by www.ccl.net (8.6.10/930601.1506) id OAA27133; Mon, 22 May 1995 14:21:03 -0400 From: Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA23777; Mon, 22 May 1995 20:09:57 +0200 Date: Mon, 22 May 1995 20:09:57 +0200 Message-Id: <9505221809.AA23777@risc1.lrm.fi.cnr.it> To: chemistry@ccl.net Subject: Fitting two parameters Dear Netters, I am looking for a program that can fit more than one parameter simultaneously and can run on a RISC station. Is there anything available through FTP? Thank you Antonio Rosato e-mail: antonio@risc1.lrm.fi.cnr.it From FOX@cmchem.chem.cmu.edu Mon May 22 18:09:00 1995 Received: from cmchem.chem.cmu.edu for FOX@cmchem.chem.cmu.edu by www.ccl.net (8.6.10/930601.1506) id RAA02214; Mon, 22 May 1995 17:57:33 -0400 From: Date: Mon, 22 May 1995 17:56:04 -0400 (EDT) To: chemistry@ccl.net Message-Id: <950522175604.20201419@cmchem.chem.cmu.edu> Subject: re: Gaussian 94 workshop, deadline extended to May 25th A few places remain and late applications/confirmations are still being accepted. INTRODUCTION TO GAUSSIAN 94: THEORY AND PRACTICE Date: June 6-9, 1995 Location: CCC Erlangen, Germany Cost: $250.00 U.S. Contact: Workshop coordinator at Gaussian, Inc. FAX: (412)279-2118 E-mail: info@gaussian.com The CCC is pleased to host "Introduction to Gaussian 94: Theory and Practice." This workshop will be presented on June 6-9, 1995 at the CCC at University of Erlangen. The workshop will cover the full range of methods available in the Gaussian 94 package with emphasis on new methods and features which make Gaussian applicable to an ever widening spectrum of questions. The workshop is structured to provide an introduction to electronic structure theory as well as a hands-on review for researchers active in the field. The workshop is open to researchers at all levels of academic, government and industrial research. Please contact the Gaussian, Inc. offices for an application and further details. Instructors: Dr. Michael J. Frisch Lorentzian, Inc. Prof. H. Bernard Schlegel Wayne State University Dr. Douglas J. Fox Gaussian, Inc. Prof. Paul Schleyer CCC Tentative Agenda Topics: Introduction to Electronic Structure Theory MCSCF Methods and Applications Geometry Optimization Techniques Electron Correlation Methods Density Functional Theory Methods Excited States via CI Singlets Thermochemistry via Model Chemistries Interpretation of Results and Molecular Properties Solvent Effects on Molecular Electronic Structure Gaussian Utilities From !rgab@trpntech.com Mon May 22 18:24:01 1995 Received: from netcomsv.netcom.com for !rgab@trpntech.com by www.ccl.net (8.6.10/930601.1506) id SAA02527; Mon, 22 May 1995 18:17:56 -0400 Received: from .UUCP by netcomsv.netcom.com with UUCP (8.6.12/SMI-4.1) id PAA16519; Mon, 22 May 1995 15:06:21 -0700 Message-Id: <199505222206.PAA16519@netcomsv.netcom.com> Date: 22 May 1995 14:45:43 -0800 From: "Richard Bone" Subject: Summary- Topological Indic Content-Type: x-see-attachments To: "CCL" x-attachments: "Topological_Indices" (type: text) Subject: Summary: Topological Indices __________________________________________________________ Richard G. A. Bone, PhD. Computational Chemist Terrapin Technologies, Inc. 750-H Gateway Blvd. South San Francisco CA 94080-7020 USA Tel. +1 (415) 244 9303 FAX +1 (415) 244 9388 E-mail rgab@trpntech.com <<<<<< Attached TEXT file follows >>>>>> Computational Chemists at large: I (or the list) received 12 replies to my query last week about available Òstand aloneÓ programs which can compute topological indices. Of these, the balance between requests for the same information and those which contributed information was, Queries: 5 Answers: 7 --- not bad for a chemistry-related list. I am summarising briefly and provide more answers of my own before appending the informative replies, as I received them. I had mentioned Oxford Molecular's "Tsar" program. This is a somewhat integrated package which computes many molecular properties, including a number of topological indices. The science is embedded in a GUI with spreadsheet format and statistical tools for analysis. MOLCONN-X is truly stand-alone and is available from: Prof. L.H.Hall, 2 Davis St., Quincy, MA 02170 He is currently distributing version 2.0 of the program. He supplied me with a list of background references to the many indices that the program computes; examples include, but are not restricted to: Chi-indices; Kappa-ÒshapeÓ indices; Electrotopological state indices; information theoretic indices; counts of particular sub-fragments, etc. There are two other programs which were mentioned (but I have yet to explore): one is S. Basak's program, POLLY (from Minnesota). E-mail sbasak@ua.d.umn.edu or sbasak@wyle.nrri.umn.edu. The other is from the group at Zagreb, e-mail sabljic@olimp.irb.hr. [I am not sure that I understand this e-mail address; Zagreb is in Croatia? '.hu' is Hungary, so what is '.hr' ? Have I lost track of how many countries/states there are in Europe at the moment?] References to the Tripos software did not really meet our needs of something which is "stand alone", though my understanding from this is that Sybyl is therefore the only one of the "Big 3" modelling packages which supports topological index calculations. References to other molecular properties and "fingerprints" were not exactly relevant to our needs. In our interpretation, "topological indices" are numerical descriptors which can be computed from 2D information (connectivity, Atomic numbers) alone. Though there are some "3D" indices which use a 3D distance-matrix. Bitstring-molecular fingerprints tend to encode a large amount of information and do not necessarily allow one to correlate properties with structure in an obvious manner. Topological indices have uses beyond simply providing Òmolecular ID numbersÓ. Thanks to all who responded. Richard Bone ====================================================================== > Original posting ... From: "Richard Bone" Subject: CCL:Topological Indices - programs To: "CCL" Sender: Computational Chemistry List Hello, Computational Chemists: We are looking for programs to calculate molecular "topological indices". The larger the number of indices that are handled, the better. A stand-alone program is most desirable, as is one which reads MDL mol/RD/SD/-files. So far, we know of "MOLCONN-X" and Oxford Molecular's "Tsar", though the latter is not really "stand-alone". As usual, please reply to me and I'll summarise if there is sufficient interest/response level. Richard Bone __________________________________________________________ Richard G. A. Bone, PhD. Computational Chemist Terrapin Technologies, Inc. 750-H Gateway Blvd. South San Francisco CA 94080-7020 USA Tel. +1 (415) 244 9303 FAX +1 (415) 244 9388 E-mail rgab@trpntech.com ====================================================================== From: jle@wavefun.com (5/17/95) To: Richard Bone From jle@toyota.wavefun.com Wed May 17 15:10:51 1995 From: "Joe Leonard" Date: Wed, 17 May 1995 15:11:01 -0700 Reply-To: jle@wavefun.com To: richard_bone.terrapin#u#com@trpntech.com Subject: Topological descriptors Richard, Spartan V3.1 and now V4.0 calculates classical and QM based QSAR descriptors, which might include some of what you're looking for. What are you seeking - area/volumes, charges, similarity indices, ? Joe P.S. It's commercial code, but it's useful commercial code :-) (and it's stuff I wrote...) ------------------------------------------------------------------------ Joe Leonard Wavefunction Inc. 18401 Von Karman, Suite 370 Irvine, CA 92715 I am a professional... 714-955-2120 do not attempt this at home. 714-955-2118 fax jle@wavefun.com ====================================================================== From sunger@crl.com Wed May 17 15:39:11 1995 Date: Wed, 17 May 1995 15:39:52 -0700 (PDT) From: Stefan Unger To: Richard Bone Subject: Re: CCL:Topological Indices - progr I If you have Sybyl, you can now get HDisq (developed by HDi, i.e.Health Designs), which has an enhanced set of topological indices. ====================================================================== From lnl@novo.dk Thu May 18 02:18:10 1995 Date: Thu, 18 May 95 11:18:17 +0200 From: lnl@novo.dk (Leif Norskov) To: richard_bone.terrapin#u#com@trpntech.com Subject: MOLCONN-X On the Computational Chemistry List you wrote: > So far, we know of "MOLCONN-X" Could you give me an email address or some other means of obtaining (preferably electronic) information about MOLCONN-X. We have some old source code and a manual that says ** Version 1.0 **, and I'd be interested in knowing if there is a newer version available. As to other sources of topological indices, I suppose you are not interested in internal "keys" generated by MACSS/ISIS or Tripos's Unity. The new "Selector" module from Tripos has quite a few indices, but it is expensive and not real handy as a stand-alone program (as I understand it). Sincerely, Leif Norskov Novo Nordisk A/S Copenhagen Denmark lnl@novo.dk ====================================================================== From chemistry-request@ccl.net Thu May 18 07:27:10 1995 Date: Thu, 18 May 1995 07:40:23 -0500 From: Boyd Subject: CCL:topological indexes To: OSC CCL Sender: Computational Chemistry List To answer Dr. Bone's query about programs that compute a lot of topological indexes, there is another program to check out. Its name is POLLY. Information about it is on page 426 of Volume 5 of "Reviews in Computational Chemistry." Don Donald B. Boyd, Ph.D. Research Professor of Chemistry Co-editor, REVIEWS IN COMPUTATIONAL CHEMISTRY Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274 U.S.A. Telephone 317-274-6891 Facsimile 317-274-4701 Internet boyd@chem.iupui.edu World Wide Web URL http://chem.iupui.edu/ ====================================================================== From henk@qsar.ritox.dgk.ruu.nl Thu May 18 01:23:30 1995 Date: Thu, 18 May 1995 10:19:59 CET To: richard_bone.terrapin#u#com@trpntech.com Subject: RE: CCL:Topological Indices - progr "Richard Bone" writes: > >Subject: Topological Indices - programs? >Hello, Computational Chemists: > >We are looking for programs to calculate molecular "topological indices". > >The larger the number of indices that are handled, the better. > >A stand-alone program is most desirable, as is one which reads MDL >mol/RD/SD/-files. > >So far, we know of "MOLCONN-X" and Oxford Molecular's "Tsar", though the latter >is not >really "stand-alone". Aleksandar Sabljic's group at the Rudjer Boskovic Institute in Zagreb, Croatia, have a program to do just that. His email address is: sasja@olimp.irb.hr .... Oops. that email address should be: sabljic@olimp.irb.hr ============================================================================== | Henk Verhaar | e-mail: henk@qsar.ritox.dgk.ruu.nl | | Research Institute of Toxicology | | | Environmental Toxicology Section | phone: +31 30 535338 | | Utrecht University, the Netherlands | fax: +31 30 535077 | ============================================================================== ====================================================================== From JJLOW@uop.com Thu May 18 07:04:07 1995 Date: Thu, 18 May 95 08:44 To: richard_bone.terrapin#u#com@trpntech.com Subject: topological indices Roger, <------------- ? "Richard", I think! I am interested for topological indices for solids, pacifically zeolites. Do you know of anyone working in this area? I have access to program written by Kier and Hall to generate connectivity and shape indices. Allied-Signal obtained it from the authors through a consulting agreement. I generates many indices. I suggest you contact the authors, if you are interested in their code. John J. Low UOP Research Center Des Plaines, IL ====================================================================== From carlos@hugin.ucsf.EDU Mon May 22 19:09:02 1995 Received: from hugin.ucsf.EDU for carlos@hugin.ucsf.EDU by www.ccl.net (8.6.10/930601.1506) id TAA03063; Mon, 22 May 1995 19:05:01 -0400 Received: by hugin.ucsf.EDU (931110.SGI/GSC4.24) id AA11342; Mon, 22 May 95 16:04:58 -0700 Date: Mon, 22 May 95 16:04:58 -0700 From: carlos@hugin.ucsf.EDU (Carlos Simmerling) Message-Id: <9505222304.AA11342@hugin.ucsf.EDU> To: CHEMISTRY@ccl.net Subject: MOIL-View 8.0 released via ftp MOIL-View 8.0 Available! MOIL-View (MOlecules at ILlinois) is a program for SGI and IBM RS/6000 workstations designed to allow the user to view and analyze molecular structures and dynamics. The program ia available via anonymous ftp, with full FORTRAN source code and documentation provided. Version 8.0 is a major upgrade from previously available versions. GENERAL FEATURES mouse and menu interface read/write coordinates in CHARMm CRD, PDB and AMBER formats OPTIONAL use of MOIL or AMBER topology files for bonding information allows rotation, translation etc. of structures display objects as lines, ribbons and/or spheres, sphere quality variable two molecules may be loaded and displayed simultaneously overlap function to minimize the RMSD of selected particles in two molecules user definable colors and particle selection text labels, fixed to particles or screen location calculate and show distances, angles and torsions find and display hydrogen bonds postscript output of structures, including ball-and-stick and space filling print monomer-based contact maps of molecules trajectory files may be read and a movie can be shown 2D-RMS postscript plots for trajectories, with user-definable overlap selection cluster analysis of trajectories, plots of clusters, clustering information trajectory modification- format conversion, frame averaging, particle removal plot trajectory data such as distances, angles, torsions, RMS, more compression algorithm for faster playback of complicated dynamics scenes support for NTSC/genlock video hardware solvent molecules can be added to a structure (shell or box) full FORTRAN source code provided for ease of modification OBTAINING MOIL-View The new anonymous ftp site for MOIL-View is munin.ucsf.edu (128.218.14.87). Log in as anonymous, type 'cd pub', and 'get MOIL-View.src.V8.SGI.tar.Z'. The IBM RS/6000 version (MOIL-View.src.7.6IBM.tar.Z) has not been fully tested. Documentation is available in postscript (MOIL-View.V8.doc.ps) and text (MOIL-View.V8.doc.txt) versions. For more information, please contact Carlos Simmerling at carlos@cgl.ucsf.edu. Comments and suggestions are welcome. ============================================================================= Carlos L. Simmerling, Ph.D. Department of Pharmaceutical Chemistry Phone: (415) 476-7900 Univ. of California San Francisco Box 0446, San Francisco, CA 94143 E-mail: carlos@cgl.ucsf.edu =============================================================================