From wall@phys.chem.ethz.ch Tue Aug 12 04:17:07 1997 Received: from bacon.ethz.ch for wall@phys.chem.ethz.ch by www.ccl.net (8.8.3/950822.1) id EAA29498; Tue, 12 Aug 1997 04:05:31 -0400 (EDT) Received: (from wall@localhost) by bacon.ethz.ch (8.8.6/8.8.6) id KAA09450; Tue, 12 Aug 1997 10:05:18 +0200 (CEST) Date: Tue, 12 Aug 1997 10:05:18 +0200 (CEST) Message-Id: <199708120805.KAA09450@bacon.ethz.ch> From: Ernst-Udo Wallenborn To: Anatoli Korkin , chemistry@www.ccl.net Subject: CCL:B3LYP for H-bonded systems In-Reply-To: <199708111327.JAA03198@qtp.ufl.edu> References: <199708111327.JAA03198@qtp.ufl.edu> Anatoli Korkin writes: >Dear CCLers, > >Does any one know references on comparative ab initio and DFT (preferably >B3LYP) studies of H-bonded systems and proton transfer? Any reviews on >this topic? H-bonded, i don't know, but you might find @ARTICLE{Jursic1996a, AUTHOR = {Branko S. Jursic}, JOURNAL = CPL, PAGES = {603-608}, TITLE = {Density functional theory study of radical hydrogen abstraction with hydrogen and hydroxyl radicals}, VOLUME = {256}, YEAR = {1996} } interesting anyway. From brain@amethyst.Chemie.Uni-Dortmund.de Tue Aug 12 08:17:09 1997 Received: from relay.Germany.EU.net for brain@amethyst.Chemie.Uni-Dortmund.de by www.ccl.net (8.8.3/950822.1) id IAA00537; Tue, 12 Aug 1997 08:14:26 -0400 (EDT) Received: from amethyst.Chemie.Uni-Dortmund.DE [129.217.221.2] by relay.Germany.EU.net with SMTP (5.61c:012/2.7.0.k-relay) id OAA04050; Tue, 12 Aug 1997 14:12:07 +0200 (MET DST) Received: by amethyst.Chemie.Uni-Dortmund.de (AIX 3.2/UCB 5.64/OCB-loki-1.0-31011995) id AA15670; Tue, 12 Aug 1997 14:14:28 +0100 From: brain@amethyst.Chemie.Uni-Dortmund.de (Christoph Schwittek) Message-Id: <9708121314.AA15670@amethyst.Chemie.Uni-Dortmund.de> Subject: ADF: AE-Fit-functions To: chemistry@www.ccl.net Date: Tue, 12 Aug 1997 14:14:26 +0100 (NFT) X-Mailer: ELM [version 2.4 PL2] Content-Type: text A questions concerning ADF: Has anybody developed fit-functions for the all-electron-basis to be used in ADF? I ask this question because we would like to do a geometry-optimization in an electric field by hand (coordinate driving) In our opinion it is important to take into account the inner shells too to explain a molecular electrostriction. Are there other opinions? From schiffer@h1tw0036.hoechst.com Tue Aug 12 10:17:10 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id JAA00777; Tue, 12 Aug 1997 09:16:39 -0400 (EDT) Received: by backup.hoechst.com id PAA06984; Tue, 12 Aug 1997 15:12:40 +0200 Received: from unknown(134.81.76.36) by backup id sma006969; Tue Aug 12 15:11:45 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id PAA02480; Tue, 12 Aug 1997 15:12:31 +0200 Message-ID: <33F0613E.794B@h1tw0036.hoechst.com> Date: Tue, 12 Aug 1997 15:12:30 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Anatoli Korkin CC: Computational Chemistry List Subject: Re: CCL:B3LYP for H-bonded systems References: <199708111327.JAA03198@qtp.ufl.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Anatoli Korkin wrote: > > Dear CCLers, > > Does any one know references on comparative ab initio and DFT (preferably > B3LYP) studies of H-bonded systems and proton transfer? Any reviews on > this topic? > > Thank you, > > Anatoli Korkin See for a very recent review : Carlo Adamo, Vincenzo Barone Structural and Dynamical Features of Hydrogen Bonds from Conventional and Hybrid Density Functional Methods in : Recent Advances in Density Functional Meythods, Part II, Ed.: Delano P. Chong, World Scientific, 1997, Chap. 5, pp. 115-164 ( Recent Advances in Computational Chemistry, Vol.1 ) -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com From comartin@wicc.weizmann.ac.il Tue Aug 12 11:17:09 1997 Received: from winston.weizmann.ac.il for comartin@wicc.weizmann.ac.il by www.ccl.net (8.8.3/950822.1) id KAA01197; Tue, 12 Aug 1997 10:23:46 -0400 (EDT) Received: from localhost by winston.weizmann.ac.il; (5.65v3.2/1.1.8.2/28Jul95-1212AM) id AA08005; Tue, 12 Aug 1997 16:59:39 +0300 Date: Tue, 12 Aug 1997 16:59:39 +0300 (IDT) From: "Jan M.L. Martin" X-Sender: comartin@winston.weizmann.ac.il To: Ernst-Udo Wallenborn Cc: Anatoli Korkin , chemistry@www.ccl.net Subject: Re: CCL:B3LYP for H-bonded systems In-Reply-To: <199708120805.KAA09450@bacon.ethz.ch> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 12 Aug 1997, Ernst-Udo Wallenborn wrote: > Anatoli Korkin writes: > >Dear CCLers, > > > >Does any one know references on comparative ab initio and DFT (preferably > >B3LYP) studies of H-bonded systems and proton transfer? Any reviews on > >this topic? Perhaps J. M. L. Martin, V. Aviyente, and C. Lifshitz, ``The insertion of amines and alcohols into proton bound dimers. A density functional study'', Journal of Physical Chemistry A 101, 2597-2606 (1997) might interest you. JM --------------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/Rechovot 76100/ISRAEL FAX +972(8)9344142 Phone +972(8)9342533 E-mail comartin@wicc.weizmann.ac.il *** research group WWW home page http://theochem.weizmann.ac.il/ *** ---- kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo l'hitfached k'lal --- From kmk4@archaeopteryx.ukc.ac.uk Tue Aug 12 13:17:12 1997 Received: from mercury.ukc.ac.uk for kmk4@archaeopteryx.ukc.ac.uk by www.ccl.net (8.8.3/950822.1) id MAA01749; Tue, 12 Aug 1997 12:30:41 -0400 (EDT) Received: from kiwi.ukc.ac.uk by mercury.ukc.ac.uk with SMTP (PP); Tue, 12 Aug 1997 17:30:00 +0100 Received: from pterodactyl.ukc.ac.uk by kiwi.ukc.ac.uk (SMI-8.6/UKC-2.14) id RAA29293; Tue, 12 Aug 1997 17:29:57 +0100 Sender: cedrik@ukc.ac.uk Message-ID: <33F08FDD.207D5579@cmr.ukc.ac.uk> Date: Tue, 12 Aug 1997 17:31:25 +0100 From: Kevin Kennedy Organization: Centre for Materials Research X-Mailer: Mozilla 3.01Gold (X11; I; Linux 2.0.30 i586) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Fe2+ - O2- potential Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi does anyone have a Buckingham potential to model the Fe2+ - O2- interatomic interaction? thanks for your time Kevin People often find it easiler to be a result of the past than a cause of the future --------------------------------------------------------------------- Chemical Physicist Tel: +1227 764000 extn 3549 Centre for Materials Research Mobile: +973 320083 The Department of Chemistry Fax: +1227 827724 The University of Kent Cyberphone: 129.12.23.136 Canterbury, Kent CT2 7NH http://cmr.ukc.ac.uk/ From intsim.com!haun@news.cts.com Tue Aug 12 19:17:13 1997 Received: from mailhub.cts.com for intsim.com!haun@news.cts.com by www.ccl.net (8.8.3/950822.1) id SAA03472; Tue, 12 Aug 1997 18:18:51 -0400 (EDT) Received: from donews.cts.com(really [192.188.72.21]) by mailhub.cts.com via smail with smtp id for ; Tue, 12 Aug 97 12:21:47 -0700 (PDT) (Smail-3.1.92 1996-Mar-19 #3 built 1996-Apr-21) Received: from intsim.com by donews.cts.com with uucp (Smail3.1.29.1 #5) id m0wyLta-00001dC; Tue, 12 Aug 97 11:42 PDT Received: from topi.intsim.com by zebra.intsim.com via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA00146; Tue, 12 Aug 97 11:36:54 -0700 Message-Id: <2.2.32.19970812184152.006aac94@zebra.intsim.com> X-Sender: haun@zebra.intsim.com X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 12 Aug 1997 11:41:52 -0700 To: chemistry@www.ccl.net From: Dan Haun Subject: SCULPT Molecular Modeling at the Desk Top Dear CCLers, Interactive Simulations, Inc., is pleased to announce the release of SCULPT R. 2.5. The new features include a 2D-3D converter and greater file compatibility. With these additions, SCULPT models small molecules and interfaces with various drawing programs. The new features include: * Copy-n-paste from ISIS/Draw and Chime * Copy-n-paste from ChemWindows, Chem3D, and ChemBuilder 3D * Tight integration with 2D and 3D builders * Accurate 2D-3D conversion * Improved force fields for small molecules (UFF) and protein-ligand interaction * Improved graphics quality and speed SCULPT still offers interactive capabilities of overlaying multiple molecules to determine similarities, twisting and turning molecular structures for conformational analysis, docking of ligands, minimizing in real-time, and visualizing H-bond, electrostatic, and van der Waals forces. SCULPT also allows copying and pasting into MS Word, and PowerPoint for documentation and presentation as well as the recording of QuickTime movies. SCULPT is available on the PC, PowerMac, and the SGI. To DOWNLOAD a free trial of SCULPT or to receive additional information, please visit Interactive Simulations, Inc.'s, Web site at http://www.intsim.com or contact us directly at 1-888-2-SCULPT (1-619-658-9462). Sincerely yours, Dan Haun Daniel P. Haun Tel: (619) 658-9462 Interactive Simulations Inc. Toll Free: (888) 272-8578 5330 Carroll Canyon Rd. Email: haun@intsim.com San Diego, CA 92121 Fax: (619) 658-9463 Web site http://www.intsim.com From JeffAyres@worldnet.att.net Tue Aug 12 23:17:16 1997 Received: from mtigwc04.worldnet.att.net for JeffAyres@worldnet.att.net by www.ccl.net (8.8.3/950822.1) id WAA04537; Tue, 12 Aug 1997 22:56:09 -0400 (EDT) Received: from LOCALNAME ([207.116.70.35]) by mtigwc04.worldnet.att.net (post.office MTA v2.0 0613 ) with SMTP id AAA5021; Wed, 13 Aug 1997 02:55:38 +0000 Message-ID: <33F12149.4F7B@worldnet.att.net> Date: Tue, 12 Aug 1997 19:51:53 -0700 From: "Jeffrey J. Ayres" Organization: independent X-Mailer: Mozilla 3.0 (Win16; I) MIME-Version: 1.0 To: chrirena@techunix.technion.ac.il CC: chemistry@www.ccl.net Subject: converting cacao output into html Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Jeffrey, Please, send a summury if you will get any answers. Thanks, Dr. Irena Efremenko chrirena@techunix.technion.ac.il Chemical Engeneering Department, Technion, Israel Institute of Technology Kyriat Technion, 32000, Haifa, Israel Tel. (972)-4-8292902 Fax. (972)-4-8230476 The first letter was the most useful. PSP, paint shop pro converts .hgl files, resolution is not as good as the orginals. In addition if size of the image is reduced too much the colors are lost and the images must be viewed in black and white. MS Word 97 is the easiest to use, however once the files are converted to .html resolution is poor. To improve the resolution for smaller size images use PSP, first resize, second crop the image using the square selection tool(should save as a .gif image) under the edit menu copy the cropped image using the paste function into a new selection, it should convert the file into a .gif file. Save the file. Gif files are readable with several browsers. The post script files mentioned by John Nash were not verifiable using my system. The post script files were not copied into files on my hard drive. Jeff Ayres MS Biochemistry Cal. State Univ. Hayward Seeking a job in computational chemistry Dear Jeff, I suppose you refer to the .hgl files produced by CACAO. You may import these files in a document with MS word 6. Moreover, PaintShop (Windows95 shareware) can read and convert these files. Beware that there are two possible HP extensions implemented in Paintshop. Sorry I do not remember now the correct extension type. You may download paintshop from ftp://ftp.support.lotus.com//pub/utils/pubutils/win32/psp32.zip Hope it helps Regards Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it the file of cacao are HPGL files, you produce them for all the picture on the screen and they are colected under /moan with the names cacao1.hgl cacao2.hgl.. and so on togheter with moan1.hgl... you can preview them with view (if you installed printgl) or you can easily import in WORD6.0 (htere is a filter for HPGL file) or in any other graphic program able to read hpgl files, then form there you may be able to convert them in .bmp or jpg I hope that his is of some help... best regards Davide Proserpio ------------------------------------------------------------------- Davide M. Proserpio Dipartimento di Chimica Strutturale e Stereochimica Inorganica Universita' di Milano, Via Venezian, 21 - 20133 Milano, Italy phone +39-2-70635120 fax 70635288 - davide@csmtbo.mi.cnr.it ------------------------------------------------------------------- Jeff- CACAO can output its pictures in PostScript and I think HPGL. (You have to have the PRINTGL package installed as well.) From there, you can use Illustrator, GhostScript, or anything else that will convert PS for the former, and I believe that PC WordPerfect will read in HPGL. On the Mac, Graphic Converter can read HPGL, too. Personally, I've had good luck with the color postscript files. Since they are "true" PostScript files, they are small and easily manipulatable (i.e. vector not bitmap). I've had the best luck using Illustrator to make my figures. Good luck! -john almost a PhD... days now.... -==-John R. Nash-==-nash@chem.wisc.edu-==-UW-Madison Chem. Dept-==- --- "When in doubt, roll!" ---