From chemistry-request@server.ccl.net Tue Jun 1 03:35:41 1999 Received: from gatekeeper2.novartis.com (gatekeeper2.novartis.com [194.191.169.74]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA21397 for ; Tue, 1 Jun 1999 03:35:34 -0400 From: alberto.gobbi@cp.Novartis.com Received: from mta1.is.chbs (mta1.novartis.com [192.37.10.90]) by gatekeeper2.novartis.com (8.9.3/8.9.3) with ESMTP id JAA03306; Tue, 1 Jun 1999 09:30:54 +0200 (MET DST) Received: from pp-banzai-chbs.cp.chbs (pp-banzai-chbs.cp.chbs [168.246.161.82]) by mta1.is.chbs (8.9.3/8.9.3) with ESMTP id JAA23400; Tue, 1 Jun 1999 09:32:16 +0200 (MET DST) Received: by pp-banzai-chbs.cp.chbs with Internet Mail Service (5.5.2448.0) id ; Tue, 1 Jun 1999 09:30:54 +0200 Message-ID: <304CAD40233FD211837B00005A422402FB4879@pp-timon-chbs.cp.chbs> To: eugene.leitl@lrz.uni-muenchen.de, CHMINF-L@LISTSERV.INDIANA.EDU Cc: chemistry@ccl.net Subject: RE: SMILES (was IUPAC rules online and ACD/Name Version 4) Date: Tue, 1 Jun 1999 09:30:52 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Hi Everybody, we are using smiles extensively in our chemical databases (daylight, ORACLE) as a key for fullstructure search. There are also a few other Chemical Editors which can create SMILES: Daylight has one, there is a free one from Peter Ertl: http://www.daylight.com/bernd-cgi/Novartis/download.cgi ChemDraw others. Cheers, Alberto -----Original Message----- From: Eugene Leitl [mailto:eugene.leitl@lrz.uni-muenchen.de] Sent: Mittwoch, 26. Mai 1999 02:59 To: CHEMICAL INFORMATION SOURCES DISCUSSION LIST Cc: chemistry@ccl.net Subject: CCL:SMILES (was IUPAC rules online and ACD/Name Version 4) I'm curious: does anybody use (unique) SMILES for nomenclature _and_ as a search key? http://www.daylight.com/dayhtml/smiles/smiles-relatives.html http://www.daylight.com/dayhtml/doc/theory/theory.toc.html I'm interested in any pointers to sources devoted to parsing, creation and other manipulation of SMILES strings. So far, I'm only aware of Babel http://www.chem.ohiou.edu/~dolata/babel.html TIA, Eugene Leitl Tony Williams writes: > There have been a number of discussions of late regarding chemical > nomenclature and some pointers to IUPAC nomenclature. For those of you > interested the IUPAC rules have been available online for a while now [...] -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Jun 1 04:49:02 1999 Received: from aleph.net.uniovi.es (aleph.net.uniovi.es [156.35.11.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA22391 for ; Tue, 1 Jun 1999 04:48:55 -0400 Received: from pinon.ccu.uniovi.es by aleph.net.uniovi.es (PMDF V5.1-11 #30226) with ESMTP id <01JBVSU2AJNA00OKN5@aleph.net.uniovi.es> for chemistry@ccl.net; Tue, 1 Jun 1999 10:38:45 +0200 (MET) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.9.2/8.9.2) id KAA20261; Tue, 01 Jun 1999 10:38:42 +0200 (METDST) Date: Tue, 01 Jun 1999 10:38:42 +0200 (METDST) From: Victor Lua~na Subject: Re: CCL:charged unit cells To: chemistry@ccl.net, owner-chemistry@server.ccl.net Message-id: <199906010838.KAA20261@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit > From owner-chemistry@server.ccl.net Mon May 31 13:48:59 MET 1999 > Date: Mon, 31 May 1999 12:45:14 -0700 (MST) > From: Alexander Hofmann > Subject: CCL:charged unit cells > X-Sender: hofmann@pcjan.chemie.uni-leipzig.de > > does anybody have experience with charged unit cells in calculations with > periodic boundary conditions? Is there a way to handle them WITHOUT the > counterion? Do you want to simulate a charged defect in a crystal? If you want to use a periodic crystal method you must introduce within the repetitive cell a second defect that neutralizes the first one. A well known alternative is to simulate the defect as a finite cluster embedded in the potential provided by the lattice. There are different embedding techniques described in the literature. If you want to use ab initio calculations, look for references by: R. Pandey, Z. Barandiaran, N.W. Winter, L. Pueyo, C. Pisani, L. Seijo, J.M. Vail, M.J. Gillan, etc. A short set of references follow. Best regards, V. Lua~na @ARTICLE{cps-POC92, author = { C. Pisani and R. Orlando and F. Cor\`{a} }, title = {On the problem of a suitable definition of the cluster in embedded-cluster treatments of defects in crystals.}, year = 1992, journal = {J. Chem. Phys.}, volume = 97, pages = 4195 } @ARTICLE{cps-WPT87b, author = { N. W. Winter and R. M. Pitzer and D. K. Temple }, journal = {J. Chem. Phys.}, volume = 87, pages = 2945, year = 1987, } @ARTICLE{cps-VPK91, author = { J. M. Vail and R. Pandey and A. B. Kunz }, journal = {Rev. Solid State Science}, volume = 5, pages = 241, year = 1991, } @ARTICLE{cps-LP89, author = { V. {Lua\~{n}a} and L. Pueyo }, journal = {Phys. Rev. B}, volume = 39, pages = 11093, year = 1989, } @ARTICLE{cps-BS88, author = { Z. {Barandiar\'{a}n} and L. Seijo }, journal = {J. Chem. Phys.}, volume = 89, pages = 5739, year = 1988, } @ARTICLE{cps-BS88, author = { J. L. Pascual and L. Seijo and Z. Barandiar\'{a}n }, title = { Ab initio model potential embedded-cluster study of Jahn-Teller parameters and electronic transition energies of Cr$^{2+}$ in oxide and fluoride octahedral coordination }, journal = {Phys. Rev. B}, volume = 53, pages = {1138--1145}, year = 1996, } @ARTICLE{cps-PDNK90, author = { C. Pisani and R. Dovesi and R. Nada and L. N. Kantorovich }, journal = {J. Chem. Phys.}, volume = 92, pages = 7448, year = 1990, } @Article{cps-FB94, author = {M. Fl\'{o}rez and M. A. Blanco and V. Lua\~{n}a and L. Pueyo}, title = {Local geometries and stabilities of Cu$^+$ centers in alkali halides}, journal = {Phys. Rev. B}, year = {1994}, volume = {49}, pages = {69--75} } @ARTICLE{cps-VG92, author = {A. De Vita and M. J. Gillan and J. S. Lin and M. C. Payne and I. \protect{\v{S}}tich and L. J. Clarke}, title = {Defect energetics in MgO treated by first-principles methods}, journal = {Phys. Rev. B}, volume = {46}, year = {1992}, pages = {12964--12973}, } @ARTICLE{cps-PC94, author = {C. Pisani and F. Cor\`{a} and R. Dovesi and R. Orlando}, title = {Embedded-cluster and supercell treatment of charged defects in crystals}, journal = {J. Electron Spectrosc. Relat. Phenom.}, volume = {69}, year = {1994}, pages = {1--12}, } -- HomePage %%http://www3.uniovi.es/~quimica.fisica/qcg/vlc/luana.html%% +----------------------------------------------+ +---^---/ / ! Victor Lua~na ! | ~ / Just in case ! Departamento de Quimica Fisica y Analitica ! | | you don't ! Universidad de Oviedo, 33006-Oviedo, Spain ! < / remember ! e-mail: %%victor@carbono.quimica.uniovi.es%% ! | / where Oviedo ! phone: (34)-8-5103491 fax: (34)-8-5103125 ! |____ ___/ is ;-) +----------------------------------------------+ \/ From chemistry-request@server.ccl.net Tue Jun 1 09:50:59 1999 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA25175 for ; Tue, 1 Jun 1999 09:50:58 -0400 Message-ID: Date: 1 Jun 1999 08:51:27 -0500 From: "Boyd" Subject: new book To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hello CCLers, We are pleased to announce the publication of Volume 13 of REVIEWS IN COMPUTATIONAL CHEMISTRY. Coverage includes: o how to treat open-shell molecules o coping with basis set superposition errors o quantum Monte Carlo (QMC) methods o water models for molecular simulations o simulation of pH-dependent properties of proteins o design of programs for chemical structure drawing o citation impact data on computational chemists The featured authors are: J. B. Anderson, J. Antosiewicz, T. Bally, W. T. Borden, J. M. Briggs, J. E. Combariza, H. E. Helson, N. R. Kestner, R. D. Mountain, and A. Wallqvist. The ISBN of Volume 13 (xxxiii + 420 pp, 1999) is 0-471-33135-X. K. B. Lipkowitz and D. B. Boyd are the editors of this book published by John Wiley & Sons, Inc., http://www.wiley.com/. Thanks to its authors, Reviews in Computational Chemistry has become the premier source for tutorials and reviews for our field. Volume 12, the prior volume, was released in October 1998. More information, including complete author and subject indexes of every volume, can be found at http://chem.iupui.edu/rcc/rcc.html. Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry Editor, Journal of Molecular Graphics and Modelling (publication of the ACS Computers in Chemistry Division) Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Mon May 31 06:48:52 1999 Received: from chris2.u-strasbg.fr (maerker@chris2.u-strasbg.fr [130.79.34.140]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA20144 for ; Mon, 31 May 1999 06:48:44 -0400 Received: (from maerker@localhost) by chris2.u-strasbg.fr (8.8.8/8.8.8) id MAA01715; Mon, 31 May 1999 12:44:22 +0200 From: Christoph Maerker Message-Id: <199905311044.MAA01715@chris2.u-strasbg.fr> Subject: Re: CCL:opt=z-matrix To: chemistry@ccl.net (ccl) Date: Mon, 31 May 1999 12:44:22 +0200 (MEST) Cc: larso@dina.kvl.dk Organization: Laboratoire de Chimie Biophysique Institut Le Bel Universite Louis Pasteur Postal-Address: 4, rue Blaise Pascal, F- 67000 Strasbourg FRANCE Phone: +33/3-88-41-53-19 Fax: +33/3-88-60-63-83 X-Mailer: ELM [version 2.4ME+ PL37 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 532 Dear Lars, you wrote: >I am performing geometry optimizations using Gaussian98 using >opt=z-matrix. My problem is that every time an angle reaches a value >larger than 180 degrees, the calculations stops. Is there a way of >avoiding this. There are, indeed, several strategies to avoid such errors. 1) Write a correct z-matrix is the best solution. I guess you have to include an additional dummy atom. 2) Use another coordinate set, e.g. internal redundant coordinates (highly recommended) or cartesians. Regards, Christoph From chemistry-request@server.ccl.net Mon May 31 11:07:27 1999 Received: from terra.ifi.unicamp.br (terra.ifi.unicamp.br [143.106.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA22375 for ; Mon, 31 May 1999 11:07:11 -0400 Received: from lua.ifi.unicamp.br (lua [143.106.6.13]) by terra.ifi.unicamp.br (8.9.3/8.9.3) with ESMTP id MAA04294 for ; Mon, 31 May 1999 12:00:48 -0300 (BSC) Received: (from daemon@localhost) by lua.ifi.unicamp.br (8.9.3/8.9.3) id MAA24730 for ; Mon, 31 May 1999 12:00:48 -0300 (BSC) Received: from marte.ifi.unicamp.br(143.106.6.10) via SMTP by lua.ifi.unicamp.br, id smtpdaayefa; Mon May 31 12:00:44 1999 Received: (from dasf@localhost) by marte.ifi.unicamp.br (8.6.9/8.6.9) id MAA10972; Mon, 31 May 1999 12:00:44 -0300 Date: Mon, 31 May 1999 12:00:44 -0300 (BSC) From: Demetrio Antonio da Silva Filho - doutorado X-Sender: dasf@marte To: chemistry@ccl.net Subject: First excited state optimization using MOPAC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I want to make an optimization using AM1-CI to optimize the first excited state. I heard that MOPAC can do this. Does anybody in this list already make calculation of this kind? Is it possible to send me one input to make it using MOPAC? Thanks, Demetrio Filho _______________________________________________________________ Demetrio A. da Silva Filho UNICAMP - IFGW Predio D - Sala 17 CEP 13083-970 C.Postal 6165 Campinas - SP - Brazil _______________________________________________________________ LEARN FROM YESTERDAY, LIVE FOR TODAY, LOOK TO TOMORROW, REST THIS AFTERNOON. -- SNOOPY From chemistry-request@server.ccl.net Tue Jun 1 11:49:55 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27102 for ; Tue, 1 Jun 1999 11:49:55 -0400 Received: from jason.MAGELLAN.UMontreal.CA (jason.MAGELLAN.UMontreal.CA [132.204.2.30]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id LAA25075 for ; Tue, 1 Jun 1999 11:45:24 -0400 (EDT) Received: from browning.ctheo.umontreal.ca (browning.CTHEO.UMontreal.CA [132.204.70.209]) by jason.MAGELLAN.UMontreal.CA (8.8.8/8.8.8) with ESMTP id LAA04336 for ; Tue, 1 Jun 1999 11:45:23 -0400 (EDT) Date: Tue, 1 Jun 1999 11:42:25 -0400 (EDT) From: "Pierre-Jean L'Heureux" X-Sender: lheureup@browning.ctheo.umontreal.ca To: chemistry@ccl.net Subject: Re: CCL:SMILES (was IUPAC rules online and ACD/Name Version 4) In-Reply-To: <304CAD40233FD211837B00005A422402FB4879@pp-timon-chbs.cp.chbs> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII MOE, a Chemical Computing Group software, does use SMILE for database searching. http://www.chemcomp.com/ _\//__ / _ _ \ ( @ @ ) +----.oOOo--()--oOOo.----------------------------------------------------+ Pierre-Jean L'Heureux |"Nous n'hritons pas la terre de nos Departement de chimie | parents, nous l'empruntons a nos Universite de Montreal | enfants." Tel: (514) 343-6111 ext:3991 | Antoine de Saint-Exupery Page:(514) 930-2946 |Email: lheureup@magellan.umontreal.ca Fax: (514) 343-2468 |http://www.centrcn.umontreal.ca/~lheureup > > I'm curious: does anybody use (unique) SMILES for nomenclature > _and_ as a search key? > > http://www.daylight.com/dayhtml/smiles/smiles-relatives.html > > http://www.daylight.com/dayhtml/doc/theory/theory.toc.html > > I'm interested in any pointers to sources devoted to parsing, creation > and other manipulation of SMILES strings. So far, I'm only aware of > Babel http://www.chem.ohiou.edu/~dolata/babel.html > > TIA, > > Eugene Leitl > > Tony Williams writes: > > There have been a number of discussions of late regarding chemical > > nomenclature and some pointers to IUPAC nomenclature. For those of you > > interested the IUPAC rules have been available online for a while now > [...] > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins >