From dmit@ncc.free.net Mon Mar 14 03:41:17 1994 Received: from unic.uni-c.dk for dmit@ncc.free.net by www.ccl.net (8.6.4/930601.1506) id DAA11963; Mon, 14 Mar 1994 03:20:34 -0500 Received: from ncc.free.net by unic.uni-c.dk (5.65c+/1.34) id AA20345; Mon, 14 Mar 1994 09:20:12 +0100 Received: from [193.124.3.22] (nmr1.ioh.free.net) by ncc.free.net with SMTP id AA16803 (5.65c8/EM.01/IDA-1.4.4 for chemistry@ccl.net); Mon, 14 Mar 1994 07:57:42 GMT From: "Dmitry E. Dmitriev" Date: Mon, 14 Mar 94 11:18:59 +0300 Message-Id: <40740.dmit@ncc.free.net> X-Popmail-Charset: IBM 8-Bit To: chemistry@ccl.net Subject: MOLGEN info wanted.. X-Russian: Cyrillic To whom it may concern 1 month ago we've got information from CCL about MOLGEN 3.0 software. We requested (via e.mail and fax which are noted in demo) Mr. Hudecek about details but until now we did not receive any answers. I'm wondering whether were are other posibilities to contact with destributers of MOLGEN 3.0 and also I would appreciate for sending me addresses of any users of this software. With best regards, Dmitry E. Dmitriev, N.D. Zelinsky Institut of Organic Chemistry, Russian Academy of Sciensis, Leninsky pr. 47, Moscow, Russia E-mail dmit@ncc.free.net tel 7 (095) 135 90 94 fax 7 (095) 135 53 28 From kreidler@clio.rz.uni-duesseldorf.de Mon Mar 14 07:41:16 1994 Received: from clio.rz.uni-duesseldorf.de for kreidler@clio.rz.uni-duesseldorf.de by www.ccl.net (8.6.4/930601.1506) id HAA13287; Mon, 14 Mar 1994 07:39:00 -0500 Received: by clio.rz.uni-duesseldorf.de (5.64/10.0) id AA21136; Mon, 14 Mar 94 13:39:41 +0100 From: kreidler@clio.rz.uni-duesseldorf.de (Kay Kreidler) Message-Id: <9403141239.AA21136@clio.rz.uni-duesseldorf.de> Subject: MOPAC 7.0 vs. MOPAC93 To: chemistry@ccl.net (Theochem-Liste) Date: Mon, 14 Mar 1994 13:39:37 +0100 (MET) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 297 Hi netters! What are the differences between MOAPC 7.0 and MOAPC93? I thought, you can calculate pKa-values with MOPAC 7.0, but we got a copy by QCPE and it seems, that this is not true. Does anyone know, how to get MOAPC93 and what its price is (I think it's commercial). Thanks Kay Kreidler From JKONG@ac.dal.ca Mon Mar 14 11:42:34 1994 Received: from SYSWRK.UCIS.DAL.CA for JKONG@ac.dal.ca by www.ccl.net (8.6.4/930601.1506) id LAA14693; Mon, 14 Mar 1994 11:36:04 -0500 Received: from AC.Dal.Ca by SYSWRK.UCIS.DAL.CA (PMDF V4.2-14 #2545) id <01H9YNRA51NK002O4S@SYSWRK.UCIS.DAL.CA>; Mon, 14 Mar 1994 12:35:57 -0400 Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.2-14 #2545) id <01H9YNL77DAU0014SN@AC.DAL.CA>; Mon, 14 Mar 1994 12:35:36 -0400 Date: Mon, 14 Mar 1994 12:35:36 -0400 From: JING KONG Subject: Yeti To: chemistry@ccl.net Message-id: <01H9YNL77DAW0014SN@AC.DAL.CA> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, Does anyone know about a molecular mechanics software called "Yeti"? How can I access it? It is probably either from David Huhta, U of Kansas, or Angelo Vedani, Swiss Institute for Alternatives to Animal Testing. Thanks! Jing Dalhousie From JKONG@ac.dal.ca Mon Mar 14 11:50:30 1994 Received: from SYSWRK.UCIS.DAL.CA for JKONG@ac.dal.ca by www.ccl.net (8.6.4/930601.1506) id LAA14649; Mon, 14 Mar 1994 11:30:39 -0500 Received: from AC.Dal.Ca by SYSWRK.UCIS.DAL.CA (PMDF V4.2-14 #2545) id <01H9YNKLW1U8002PSZ@SYSWRK.UCIS.DAL.CA>; Mon, 14 Mar 1994 12:30:29 -0400 Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.2-14 #2545) id <01H9YNHMFNOG0014SN@AC.DAL.CA>; Mon, 14 Mar 1994 12:30:14 -0400 Date: Mon, 14 Mar 1994 12:30:13 -0400 From: JING KONG Subject: Summary: H-bonds To: chemistry@ccl.net Message-id: <01H9YNHMM35U0014SN@AC.DAL.CA> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, Here is the summary of the responses I got for my query about the bond lengths and directionalities of h-bonds. Personally, I found Konrad Koehler's list is helpful. For ab initio studies, Dr. Scheiner has some good reviews. But I have not checked through all the references yet. Here is my new question: how to access to Cambridge Crystallographic Data Base and Brookhaven Data Base? Thank you all who responsed! Jing Dalhousie ------Cut here------------------- From: IN%"b130778@hp720a.csc.cuhk.hk" "MA NGAI LING IDA" 10-MAR-1994 23:11:50.82 To: IN%"JKONG@ac.dal.ca" CC: Subj: RE: CCL:H-bonds Check out papers by Janet Del Bene. I think she has done quite a few H-bond compounds. Ida From: IN%"dave@mercury.chem.csiro.au" "Dave Winkler" 11-MAR-1994 00:35:53.54 To: IN%"JKONG@ac.dal.ca" "JING KONG" CC: Subj: RE: CCL:H-bonds The best way is to search the Cambridge Crystallographic database (>100,000 compounds) for all hydrogen-bonded structures. Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From: IN%"frj@dou.dk" "Frank Jensen" 11-MAR-1994 02:56:35.38 To: IN%"jkong@ac.dal.ca" CC: Subj: h-bond Check one of the very recent issues of JACS (marts 1994). There is an analysis of H-bonds, I can't remember the authors names. Frank From: IN%"simonson@zinfandel.u-strasbg.fr" 11-MAR-1994 03:25:07.58 To: IN%"JKONG@ac.dal.ca" CC: Subj: RE: CCL:H-bonds Take a look at the book: Hydrogen bonding in biological structures, by G. Jeffrey and W. Saenger (1991 or 1992) (Springer-Verlag I think) Tom Simonson From: IN%"kit1@molecular-recognition.chemistry.cambridge.ac.uk" 11-MAR-1994 04:58:16.63 try The geometry of the N-H...O=C H-bond,part 3, H-bond distances and angles R. Taylor, O. Kennard, W. Versichell Acta Cryst. (1984) B40 280-288 This is a good reference as it looked at many structures from the cambridge crystal database. Keith Trollope. From: IN%"heuer@tmcws1.chemie.uni-hamburg.de" 11-MAR-1994 06:38:54.22 In the first vol. of Reviews in Computational Chemistry is a artical on H-bonds derived from CSD x-ray structural database. I hadn`t the reference but the editors anonnce the vol.4 briefly on this list. The publischer was Springer and they editors Bloyd and Lipkowitz. (If i spell the name incorrect, sorry. I hope it helps Joerg R.P. Heuer Inst. fuer Pharmazie heuer@chemie.uni-hamburg.de From: IN%"KOEHLER@IRBM.IT" "Konrad, IRBM Chemistry, +39-6-91093606" 11-MAR-1994 07:59:28.77 Here are some references mainly dealing with geometries and energetics of protein-water and protein-ligand hydrogen bonding interactions. I hope you find them useful. (1) Boobbyer, D. N.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J. Med. Chem. 1989, 32, 1083-94. (2) Ippolito, J. A.; Alexander, R. S.; Christianson, D. W. Hydrogen bond stereochemistry in protein structure and function. J. Mol. Biol. 1990, 215, 457-71. (3) Murray-Rust, P.; Glusker, J. P. Directional hydrogen bonding to sp2 and sp3-hybridized oxygen atoms and its relevance to ligand-macromolecular interactions. J. Am. Chem. Soc. 1984, 106, 1018-1025. (4) Thanki, N.; Thornton, J. M.; Goodfellow, J. M. Distributions of water around amino acid residues in proteins. J. Mol. Biol. 1988, 202, 637-57. (5) Tintelnot, M.; Andrews, P. Geometries of functional group interactions in enzyme-ligand complexes: guides for receptor modelling. J. Comput.-Aided Molec. Des. 1989, 3, 67-84. (6) Vedani, A.; Dunitz, J. D. Lone-pair directionality in H-bond potential functions for molecular mechanics calculations. J. Am. Chem. Soc. 1985, 107,7653-7658. (7) Vedani, A.; Hutha, D. W. An algorithm for the systematic solvation of proteins based on the directionality of hydrogen bonds. J. Am. Chem. Soc. 1990, 112, 4759-4767. (8) Vedani, A.; Huhta, D. W. A new force field for modeling metalloproteins. J. Am. Chem. Soc. 1991, 113, 5860-5862. ------------------------------------------------------------------ | Konrad Koehler | Computational Chemistry Group | | internet: koehler@irbm.it | Department of Medicinal Chemistry | | | IRBM | | telephone: +39-6-910-93606 | Via Pontina Km. 30,600 | | fax: +39-6-910-93225 | 00040 Pomezia (Roma) | | | Italy | ------------------------------------------------------------------ From: IN%"stoutepf@chemsci1.es.dupont.com" 11-MAR-1994 09:38:41.74 I did an extensive analysis of hydrogen bonds in crystal structures and observed in MD simulations of liquid methanol. Relevant publications are: * P.F.W. Stouten & J. Kroon, "Hydrogen Bonds in Concreto and in Computro," J. Mol. Struct. 177 (1988) 467-475. * P.F.W. Stouten, B.P. van Eijck & J. Kroon, "Hydrogen Bonds in Concreto and in Computro: The Sequel," J. Mol. Struct. 243 (1991) 61-87. Please give me your physical address if you want reprints. Cheers, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- ARA/Fax: +1 (302) 695 4324 || Poul Anderson E-mail: stoutepf@chemsci1.es.dupont.com || Internet Shogi Server: kzinti || From: IN%"chp1aa@surrey.ac.uk" "Mr Andrew D Allen" 11-MAR-1994 10:41:44.21 Try looking through th brookhaven database, for protein structures which have explicitly noted hydrogen bonds. The ftp site is pdb.pdb.bnl.gov. Andy. -- ################################################################################ Structural and Computation Chemistry Group__________chp1aa@uk.ac.surrey - JANET. Department of Chemistry_____________________________phone__+44(483)-300800-2632. University of Surrey________________________________fax_________+44(483)-300803. Guildford, Surrey, GU2 5XH, UK______________________fpt____________131.227.110.2 ################################################################################ From: IN%"mn1@helix.nih.gov" 11-MAR-1994 11:53:29.31 Publications discussing/listing H-bond-lengths and directions (among others): (1) Jeffrey, G.A.; Saenger, W. Hydrogen Bonding in Biological Structures, Springer, Berlin Heidelberg, 1991. (2) Murray-Rust, P.; Glusker, J.P. Directional Hydrogen Bonding to sp2- and sp3-Hybridized Oxygen Atoms and Its Relevance to Ligand-Macromolecule Interactions, JACS 106 (1984), 1018-1025. (3) Chakrabarti, P. Anion binding sites in protein structures, J. Mol. Biol. 234 (1993), 463-482. (4) Steiner, T.; Saenger, W. Geometry of the Carbon-Hydrogen....Oxygen Hydrogen Bonds in Carbohydrate Crystal Structures. Analysis of Neutron Diffraction Data. JACS 114 (1992), 10146-10154. ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 Bethesda, MD 20892 ------------------------------------------------------------------------ From: IN%"zheng@violet.berkeley.edu" 11-MAR-1994 13:43:24.74 To: IN%"jkong@ac.dal.ca" CC: Subj: H-bond Hi, Jing, For theoretical work, please check J. Comput. Chem. 1992, 13, 1151-1169. For experimental data, please check the references cited in this paper. Yajun Zheng From: IN%"ukreis@sfu.ca" "Uwe Claus Kreis" 11-MAR-1994 15:39:22.01 A search of (HYDROGEN + BOND + STRUCTURE) gave 84 hits in UnCover. You might want to check out the following: ----------------------------------------------------UnCover-------------------- AUTHOR(s): Gilli, Paola. Bertolasi, Valerio. Ferretti, Valeria. TITLE(s): Covalent Nature of the Strong Homonuclear Hydrogen Bond. Study of the O--H--O System by Crystal Structure Correlation Methods. In: Journal of the american chemical society. FEB 09 1994 v 116 n 3 Page: 909 ----------------------------------------------------UnCover-------------------- AUTHOR(s): Wade, Rebecca C. Clark, Kevin J. Goodford, Peter J. TITLE(s): Further Development of Hydrogen Bond Functions for Use in Determining Energetically Favorable Binding Sites on Molecules of Known Structure. 1. Ligand Probe Groups with the Ability To Form Two Hydrogen Bonds. In: Journal of medicinal chemistry. JAN 08 1993 v 36 n 1 Page: 140 TITLE(s): Further Development of Hydrogen Bond Functions for Use in Determining Energetically Favorable Binding Sites on Molecules of Known Structure. 2. Ligand Probe Groups with the Ability To Form More Than Two Hydrogen Bonds. In: Journal of medicinal chemistry. JAN 08 1993 v 36 n 1 Page: 148 ----------------------------------------------------UnCover-------------------- AUTHOR(s): Mortimer, M. Moore, E.A. Healy, A. TITLE(s): A comparison of ab initio, NMR and diffraction results for a strong OHF hydrogen bond. In: Journal of molecular structure. AUG 15 1992 v 271 n 1 / 2 Page: 149 ----------------------------------------------------UnCover-------------------- AUTHOR(s): Plass, M. Kolbe, A. TITLE(s): Conformational influence on hydrogen bond. In: Journal of molecular structure. MAR 01 1992 v 267 Page: 21 ----------------------------------------------------UnCover-------------------- AUTHOR(s): Legon, A. C. Millen, D. J. TITLE(s): The nature of the hydrogen bond to water in the gas phase. In: Chemical society reviews. MAR 01 1992 v 21 n 1 Page: 71-78 ----------------------------------------------------UnCover-------------------- AUTHOR(s): Feil, D. TITLE(s): The electron density distribution in the hydrogen bond. A quantum chemical and crystallographic study. In: Journal of molecular structure. SEP 15 1990 v 237 Page: 33 ----- A. Vedani compiled a lot of structural information about H-bonds. I'm not sure where and whether he published that, but check: A. Vedani, D.W. Huhta, S.P. Jacober, JACS 111 (1989) 4075. ----- Hope this helps. Cheers, Uwe ------------------------------------------------------------------------------ - - -> Dr.-Ing. Uwe C. Kreis - -> Department of Chemistry Tel. (Int) 604 291 5650 <- -> Simon Fraser University FAX: (Int) 604 291 3765 <- -> Burnaby, B.C. V5A 1S6 E-Mail: uwe_kreis@sfu.ca <- -> Canada E-Mail: ukreis@sfu.ca <- - - ------------------------------------------------------------------------------ From: IN%"scheiner@qm.c-chem.siu.edu" 11-MAR-1994 19:39:30.59 i saw your query about h-bonds over the theoretical chem bulletin board. there are probably numerous reviews of h-bonds around. i know of one that i myself wrote not too long ago. S. Scheiner, "Ab Initio Studies of Hydrogen Bonding" in Theoretical Models of Chemical Bonding, Ed. Z. B. Maksic, Springer-Verlag, Berlin, Part 4, 1991, pp. 171-227. While not encyclopedic, it does cover a fairly wide range of different H-bonds, at least as far as ab initio calculations go. another review is; S. Scheiner, "Calculating the Properties of Hydrogen Bonds by Ab Initio Methods" in Reviews in Computational Chemistry, Eds. D. Boyd and K. Lipkowitz, VCH Publishers, New York, 1991, pp. 165-218. this one is less encyclopedic but talks more about how to do such calculations and what one might expect from the results. if you have trouble finding these in your library, i would be happy to mail you a copy. ----- Steve Scheiner, Professor scheiner@qm.c-chem.siu.edu Dept. of Chemistry & Biochemistry MailCode 4409 Southern Illinois University Carbondale, IL 62901-4409 ph: 618/453-6476 fax: 618/453-6408 From: IN%"MARTIN@cmda.abbott.com" "MARTIN%CMDA" 12-MAR-1994 12:36:22.49 We summarized a lot in a paper we wrote using such information. However, there are some nice reviews by the folks from Cambridge Structural Database & from protein crystallographers. Let me see if I can get the references now... Murray-Rust, P. Glusker, J. P. J. Am. Chem. Soc. 106 (1984) 1018. Taylor, R., Kennard, O. Acc. Chem. Res. 17 (1984) 320. Boobbyer, D. N. A., Goodford, P. J., McWhinnie, P. M., Wade, R. C. J. Med. Chem., 32 (1989) 1083. Vedani, A., Dunitz, J. D. J. Am. Chem. Soc. 107 (1985) 7653. Jeffrey, G. A., Saenger, W. Hydrogen Bonding in Biological Structures. Springer-Verlag, Berlin 1991 Let me know if you find better ones. Yvonne Martin From freeman@mozart.chm.uri.edu Mon Mar 14 14:42:35 1994 Received: from bach.chm.uri.edu for freeman@mozart.chm.uri.edu by www.ccl.net (8.6.4/930601.1506) id NAA15701; Mon, 14 Mar 1994 13:52:27 -0500 Received: from mozart.chm.uri.edu by bach.chm.uri.edu via SMTP (931110.SGI/920502.SGI) for chemistry@ccl.net id AA13540; Mon, 14 Mar 94 13:52:09 -0500 Received: by mozart.chm.uri.edu (931110.SGI/920502.SGI) for @bach.chm.uri.edu:doll@carlo.chem.brown.edu id AA18265; Mon, 14 Mar 94 13:52:08 -0500 Date: Mon, 14 Mar 94 13:52:08 -0500 From: freeman@mozart.chm.uri.edu (David L. Freeman) Message-Id: <9403141852.AA18265@mozart.chm.uri.edu> To: chemistry@ccl.net Subject: Chemical Physics Preprint Archive Cc: doll@carlo.chem.brown.edu This is to announce a chemical physics preprint archive on the World Wide Web. Those having network access to the Mosaic program can attach to the archive at URL: http://www.chem.brown.edu/chem-ph.html Operational since March 10, 1994, this database is a joint effort by the Department of Chemistry at Brown University and the Theoretical Chemistry and Molecular Physics Group at the Los Alamos National Laboratory. It has been made possible by funding >from the Camille and Henry Dreyfus Foundation. We would like to acknowledge the assistance of Paul Ginsparg at Los Alamos National Laboratory, whose programming skills and generous cooperation have made this database possible. This database has been designed to be a useful and freely available tool for education and research. The purpose of the archive is to provide an efficient means for rapidly distributing preprints to the international chemical physics community. The community is encouraged to avail themselves of the service. **************************** David L. Freeman * Department of Chemistry * University of Rhode Island * Kingston, RI 02881 * **************************** freeman@mozart.chm.uri.edu * (401) 792-5093 [office] * (401) 792-5072 [FAX] * **************************** From apa@adfa.oz.au Mon Mar 14 18:41:23 1994 Received: from sserve.cc.adfa.oz.au for apa@adfa.oz.au by www.ccl.net (8.6.4/930601.1506) id SAA17434; Mon, 14 Mar 1994 18:22:16 -0500 Received: from [131.236.60.11] (apamac.ch.adfa.oz.au) by sserve.cc.adfa.oz.au (5.67a/1.34) id AA10729; Tue, 15 Mar 1994 09:22:03 +1000 Date: Tue, 15 Mar 1994 09:22:03 +1000 Message-Id: <199403142322.AA10729@sserve.cc.adfa.oz.au> X-Sender: apa@pop.cc.adfa.oz.au Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: apa@adfa.oz.au (Alan Arnold) Subject: Australian WWW server for electronic Resources in Chemistry Announcing an Australian WWW site for electronic resources in Chemistry and related disciplines. Point your browser at http://apamac.ch.adfa.oz.au/ The site is designed to serve the Australian networked chemical community as a comprehensive 'repository?' for teaching &/or research related resources. Please have a look and send constructive criticism re style, suggestions for inclusion/deletion, updates etc to apa@adfa.oz.au. Please note that the MacHTTP server is currently running on a tired old MacII and can only handle 8 connected users so if at first you don't succeed, wait a while and try again! ---- Alan Arnold, Chemistry Department, University College (UNSW) Australian Defence Force Academy, CANBERRA ACT 2601 Australia voice:+61 6 268 8080 fax:+61 6 268 8002 e-mail: apa@adfa.oz.au web: http://apamac.ch.adfa.oz.au/ From eslone@mason1.gmu.edu Mon Mar 14 21:41:25 1994 Received: from mason1.gmu.edu for eslone@mason1.gmu.edu by www.ccl.net (8.6.4/930601.1506) id VAA18008; Mon, 14 Mar 1994 21:11:41 -0500 Received: by mason1.gmu.edu (5.65/DEC-Ultrix/4.3/GMUv3) id AA01456; Mon, 14 Mar 1994 21:11:42 -0500 Message-Id: <9403150211.AA01456@mason1.gmu.edu> Subject: Looking for... To: chemistry@ccl.net Date: Mon, 14 Mar 1994 21:11:41 -0500 (EST) From: "J. Eric Slone" Cc: CHEMED-L%UWF.BITNET@uga.cc.uga.edu X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1208 I'm looking for the following programs, preferable free or close to it, to be used for educational purposes. Any assistance would be greatly appreciated. 1 Provide predictions of proton NMR shifts. I would prefer something which would accept *any* compound and make a prediction. 2 Provide predictions on mass spec fragmentation/rearrangement patterns. Again, the ability to accept *any* compound would be ideal. They need to be PC programs, either DOS or Windows. I've seen the proton NMR program for the Mac, and would like to find a PC version of it if possible. Thanks in advance for your help, Eric ________________________________________________________________________________ J. Eric Slone Scientific Consulting Services Serving Government & Industry Since 1982 Internet: eslone@mason1.gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Voice: (703) 461-7078 Miguel do Unamuno ________________________________________________________________________________