From peon@medchem.dfh.dk Thu Oct 16 06:30:58 1997 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id GAA21661; Thu, 16 Oct 1997 06:30:09 -0400 (EDT) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.8.6/8.6) with SMTP id MAA26403; Thu, 16 Oct 1997 12:30:08 +0200 (METDST) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id NAA01946; Thu, 16 Oct 1997 13:53:51 +0200 Message-Id: In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 16 Oct 1997 12:30:11 +0200 To: Marc.Prosenc@uni-konstanz.de (Marc-Heinrich.Prosenc) From: Per-Ola Norrby Subject: Re: CCL:vibration spectras from force-field calculations Cc: CHEMISTRY@www.ccl.net Dear Marc, >it would be kind if anyone could tell me if there exist a program that >calculates >vibrational spectras from forcefields like MM2 or DISCOVER or HYPERCHEM >.... for free ? > >do there any public domain routines exist, which are able to refine >existing forcefields >like mm2 or amber when the IR-spectrum is given ? You should look up Tinker, from Jay Ponders lab. Check it out at: http://dasher.wustl.edu/tinker It's pretty hard to use IR spectra in the parameterization, and anyway, MM2 and AMBER aren't built to reproduce IR spectra. A few molecular mechanics force fields are, for example MM3 (available in Tinker) and CFF. In any case, I recommend parameterizing from a quantum chemical Hessian directly, not from the actual spectrum (a bit hard to do if what you have is the experimental spectrum :-). In most cases, it's almost hopeless to match normal modes between calculated and experimental spectrum, whereas the Hessian elements are well defined. Look up the work of Lifson & Warshel (CFF), Rasmussen (CFF-Lyngby), Hagler (CFF9x), Halgren (MMFF), ... Best Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From ng570@talisker.pnl.gov Thu Oct 16 17:31:05 1997 Received: from talisker.pnl.gov for ng570@talisker.pnl.gov by www.ccl.net (8.8.3/950822.1) id QAA24632; Thu, 16 Oct 1997 16:44:38 -0400 (EDT) Received: (from ng570@localhost) by talisker.pnl.gov (8.7.1/8.7.1) id NAA04556 for chemistry@www.ccl.net; Thu, 16 Oct 1997 13:43:57 -0700 (PDT) From: Kirk "A." Peterson Message-Id: <199710162043.NAA04556@talisker.pnl.gov> Subject: H2O Conference To: chemistry@www.ccl.net Date: Thu, 16 Oct 1997 13:43:57 -0700 (PDT) X-Mailer: ELM [Revision: 213.1] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Forwarded to the list for Pavel Rosmus. -- Kirk A. Peterson Assistant Professor Affiliate Senior Research Scientist Department of Chemistry & Theory, Modeling, and Simulation Washington State University Environmental Molecular Sciences Laboratory Richland, WA Pacific Northwest National Laboratory ------------------------------------------------------------------------------- > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ __ _ _ _ _ _ _ _ > |_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|__|_|_|_|_|_|_|_| > |_| |_| > |_| First Circular |_| > |_| |_| > |_| International Conference on |_| > |_| |_| > |_| WATER IN THE GAS PHASE |_| > |_| to be held on |_| > |_| Sunday, June 21 - Wednesday, June 24, 1998 |_| > |_| in the Ministery of Research and Education, |_| > |_| PARIS, FRANCE |_| > |_| |_| > |_|_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ __ _ _ _ _ _ _|_| > |_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|__|_|_|_|_|_|_|_| > > > LOCAL ORGANIZING COMMITTEE > > Paul Bagus > Gilberte Chambaud > Pavel Rosmus > __ __ __ __ __ __ __ > / / / / / / / / / / / / / / Universite de Marne-la-Vallee > / / / / / / / / / / // / Boulevard Descartes (Bat. M2) > / / / / / / / / / / / / / F-77420 Champs sur Marne, France > / /__/ / / / / / / /_ / / Tel. +33-1-60957304 /FAX +33-1-60957320 > /______/ /_/ /_/ /___/ /_/ e-mail: h2o@alpha.univ-mlv.fr > > INTERNATIONAL COMMITTEE > > Peter Bernath, University of Waterloo, Canada > David Clary, University College London, U.K. > Jean-Marie Flaud, University of Orsay, France > Steve Langhoff, NASA, Ames Field, USA > Claude Leforestier, University of Montpelier, France > Wilfried Meyer, University of Kaiserslautern, Germany > David Nesbitt, JILA, Boulder, USA > Martin Quack, ETH Zurich, Switzerland > Laurence Rothman, Harvard-Smithonian Center, USA > Richard Saykally, UC, Berkeley, USA > Jonathan Tennyson, University College London, U.K. > Ad van der Avoird, University of Nijmegen, Netherlands > Michel Vervloet, University Orsay, France > > SCIENTIFIC PROGRAM > > The conference on "Water in the Gas Phase" will deal with a wide range of > scientific aspects of the properties and structure of water and water > nanoclusters in the gas phase. Topics which are in the areas of > astrophysical and spectroscopic studies will form a major part of the > conference presentations; stress will also be placed on studies of > reactivity and dynamics. In all of these areas, emphasis will be given to > both experimental and theoretical efforts. > > > Studies of water and water clusters are part of a rapidly growing, > dynamic field of research. Areas of current interest in astrophysics > include studies of the sun and of comets and studies of the stellar > atmospheres of oxygen rich stars. Other exciting topics of research are > simulations of combustion processes to better understand the role of > water; the role of chromophores in water clusters in contributing to ozone > depletion; and the transition from clusters to the liquid state. A major > goal of the conference is to stimulate interactions and collaborations > between scientists working in the diverse areas of this exceptionally > broad multidisciplinary field. We expect the meeting to foster much closer > contact among astrophysicists, spectroscopists, atmospheric chemists, and > combustion chemists. In particular, the meeting has been structured to > demonstrate the great value of interactions between theorists and > experimentalists. > > The presentations at the conference have been divided into the following > major categories: H2O; H2O+; H2O nanoclusters; Charged H2O nanoclusters; > and Molecular dynamics of water clusters. The list of confirmed invited > speakers with, when available, the tentative titles of their talks is > attached at the end of this circular. Participants are invited to submit > abstracts for short oral and for poster presentations. The deadline for > the submission of these abstracts is 1 April, 1998. Authors will be > notified before 1 May whether their contributions have been accepted for > an oral or a poster presentation. > > > > Location and Dates of the Conference: > > The conference will be held in the auditorium of the Ministry of Research > and Education which is in the center of Paris. It is located in the > Quatier Latin, Paris V, near Metro stop Cardinal Lemoine. The auditorium > is well equiped for our meeting and lunch will be available for > participants at the Ministry's cafeteria. > > Registration will be possible on Sunday. The first session of > the meeting will be on Sunday, 21 June 1998 and the last session on > Wednesday, 24 June. > > Accommodation: > > Information on hotels in Paris is available on the WWW at > http://www.atcom-multimedia.fr/hotel/. Hotels in the 5th and 6th > Arrondissements of Paris, the Latin Quarter, will be convenient to the > meeting, either within walking distance or a short ride on the Paris > Metro. Please note that in June 1998 there will be the World Championship > in Soccer in Paris. This will certainly attract many visitors and hotel > reservations should be made very early. We are willing to help young > researchers to find simple but inexpensive accomodations in Paris. If you > wish help to find such accomodations, please send an e-mail to > h2o@alpha.univ-mlv.fr indicating the dates that you will stay and whether > you will be sharing your room. > > > Dates: > > 2nd circular: February 1998. > ------------- > > Deadline for final registration and submission of abstracts: > ------------------------------------------------------------ > April 1st 1998. > > > 3rd circular with meeting information: End of May 1998. > -------------------------------------- > > Fees: ----- The registration is 850 FF. This will include lunches at the > conference site. For a small number of people with very limited funds, the > registration fee may be waived. It is expected that only students will > apply to have their fees waived. > > More precise information will be given in the second circular. > > WWW home page: > -------------- > The conference has a home page on the World Wide Web > > http://alpha.univ-mlv.fr:8080/waterconference.html > > This page will be updated regularly. > > > Preregistration: > ---------------- > You should preregister before January 1st 1998. > > If possible please use the fill-out-form of the WWW home page > of the conference (see above) for preregistration. > > You can also fill in the attached form and e-mail it to > > h2o@alpha.univ-mlv.fr > > or mail or FAX it to > H2O/c.o. Pavel Rosmus > Universite de Marne-la-Vallee > Boulevard Descartes (Bat. M2) > F-77420 Champs sur Marne, France > FAX +33-1-60957320 > > > ----------------------------------------------------------------------- > Confirmed Invited Speakers > > **** H2O > > Astrophysics > Jacques Crovisier, Observatoire de Paris, France > "H2O in comets" > David Neufeld, John Hopkins University, U.S.A. > "Water in shocked clouds and elsewhere" > Spectroscopy > Peter Bernath, University of Waterloo, Canada > title to be announced > Oleg Polyansky, UCL, U.K. > "Analysis of hot water spectra in sunspots and the laboratory" > Claude Camy-Peyret and Jean-Marie Flaud, University Orsay, France > "Low pressure flame H2O spectra" > Theory > Jonathan Tennyson, UCL, U.K. > "First principle calculation of the spectrum of hot water" > David Schwenke, NASA, Ames Field, U.S.A. > "Ab initio calculations of water line strengths" > Larry Rothman, Harvard-Smithonian Center, U.S.A. > title to be annouced > L.H. Coudert, Universite d'Orsay, France > title to be annouced > Reactivity > F. Fleming Crim, University of Wisconsin, U.S.A. > "Reactivity of water" > > Reinhard Schinke, MPI Goettingen, Germany > "Photodissociation of water" > > **** H2O+ > > Astrophysics > Barry L. Lutz, Nothern Arizona University, U.S.A. > H2O+ in comets > Spectroscopy > Michel Vervloet, Universite d'Orsay, France > Spectroscopy of H2O+ > Theory > Pavel Rosmus, UMLV, France > "Renner-Teller spectra and transition probabilities of H2O+" > > **** H2O nanoclusters > > Spectroscopy > Friedrich Huisken, MPI Goettingen, Germany > "Vibrational spectroscopy of free and adsorbed water" > David Nesbitt, JILA, Boulder, USA > title to be annouced > Martin Quack, ETH Zuerich, Switzerland > title to be announced > Welford Casteleman, Pennsylvania State University, U.S.A. > title to be announced > Samuel Leutwyler, University of Bern, Switzerland > title to be announced > Richard Saykally, UC, Berkeley, U.S.A. > "Studies of water clusters by terahertz and IR > cavity ringdown spectroscopy: force fields > Theory > N.C. Handy, University of Cambridge, U.K. > "Potential energy functions for water clusters" > M. Parrinello, MPI Stuttgart, Germany > "Ab initio simulation of proton transfer and water clusters" > Ad van der Avoird, University of Nijmegen, The Netherlands > " Tunneling dynamics and spectra of water clusters" > Claude Leforestier, Universite de Montpelier, France > "Vibration rotation tunneling in the water dimer" > Zlatko Bacic, New York University, U.S.A. > title to be annouced > > **** Charged H2O nanoclusters > > Spectroscopy > Jim Coe, Ohio State University, U.S.A. > "OH- and H3O+ recombination as a function of water solvent" > Kit Bowen, John Hopkins University, U.S.A. > "Dipole bound clusters of water" > Theory > Elise Kochansky, Universite de Strasbourg, France > "Study of electronic states of H5O2+" > > **** Molecular dynamics of water clusters > > Peter Rossky, University of Texas, U.S.A. > "Molecular dynamics in water clusters" > M. Klein, University of Pennsylvania, U.S.A > "MD studies of the system H2O/HCl" > > > > ------------------------------------------------------------------ > PREREGISTRATION FORM > The International Conference on Water in the Gas Phase > Paris, France, June 21 -24, 1998 > > Please use BLOCK LETTERS or typewriter > > Last name: ________________________________________________________ > > First name: ________________________________________________________ > > Department: ________________________________________________________ > > Institution: ________________________________________________________ > > Street address: ________________________________________________________ > > Postal code: ______________ City: ___________________________________ > > State: ______________________ Country: ________________________ > > Telephone: ______________________ Fax: ________________________ > > Electronic mail: ________________________________________________________ > > I plan to attend the meeting |_| > > I would like to receive the second circular |_| > > I would like to present oral|_| or poster |_| contribution > From beroza@info.combichem.com Thu Oct 16 20:31:07 1997 Received: from info.combichem.com for beroza@info.combichem.com by www.ccl.net (8.8.3/950822.1) id UAA25256; Thu, 16 Oct 1997 20:14:26 -0400 (EDT) Received: from surf by info.combichem.com via SMTP (940816.SGI.8.6.9/940406.SGI) for id RAA17790; Thu, 16 Oct 1997 17:33:48 -0700 Message-Id: <3.0.3.32.19971016170637.0095d530@leonardo.info.combichem.com> X-Sender: pberoza@leonardo.info.combichem.com X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Thu, 16 Oct 1997 17:06:37 -0700 To: CHEMISTRY@www.ccl.net From: Paul Beroza Subject: 2D chemical structure generation Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi All, I have a molecule (several molecules actually) in an SD formatted file. The connectivity and stereochemistry are correct, but the coordinates are bogus. Is there a program out there that can generate reasonable looking 2-D coordinates (preferably in SD format) for the compounds? Alternatively, is there a program that can convert a set of SMILES strings in a file to reasonable looking 2-D structures in SD format (with the proper stereochemistry)? Thanks for the help, Paul Beroza CombiChem, Inc. beroza@info.combichem.com From katz@indigo.ucdavis.edu Thu Oct 16 21:31:08 1997 Received: from indigo.ucdavis.edu for katz@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id UAA25292; Thu, 16 Oct 1997 20:31:30 -0400 (EDT) Received: from indigo.ucdavis.edu by indigo.ucdavis.edu via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id RAA13850; Thu, 16 Oct 1997 17:33:19 -0700 Date: Thu, 16 Oct 1997 17:33:19 -0700 (PDT) From: Daniel Katz To: chemistry@www.ccl.net Subject: Code for overlapping STOs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII IS there a free and non obscure piece of code (preferably C) for calculating the overlap integrals between two Slater-Type-Orbitals (single zeta, radial part, angular parts are real spherical harmonics for s,p, and d)? I have the MOPAC FORTRAN routines, but they are not clear to me. Thanks in advance. Daniel J. Katz UC Davis, Dept. of Chemistry katz@indigo.ucdavis.edu