From sps@gamma.dou.dk Wed Sep 11 04:11:00 1996 Received: from gamma.dou.dk for sps@gamma.dou.dk by www.ccl.net (8.7.5/950822.1) id DAA06772; Wed, 11 Sep 1996 03:37:07 -0400 (EDT) Received: (from sps@localhost) by gamma.dou.dk (8.6.10/8.6.10) id JAA29551; Wed, 11 Sep 1996 09:37:05 +0200 Date: Wed, 11 Sep 1996 09:37:05 +0200 (METDST) From: "Forskningsadjunkt Ph.D. Stephan P.A. Sauer" To: chemistry@www.ccl.net Subject: CCL:PH3 potential energy surface Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I am looking for an ab initio potential surface for PH3. Stephan ------------------------------------------------ | Forskningsadjunkt Ph.D. Stephan P.A. Sauer | | Department of Chemistry, Odense University | | Campusvej 55, DK-5230 Odense M, Denmark | | Tel : +45-65572587 | | Fax : +45-66158780 | | E-mail : sps@dou.dk | | http://www.ou.dk/Nat/chem/staff/sci/Sps.html | ------------------------------------------------ From owner-chemistry@ccl.net Wed Sep 11 04:25:07 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id DAA06810; Wed, 11 Sep 1996 03:49:50 -0400 (EDT) Received: from kauno.helsinki.fi for SUNDIUS@phcu.helsinki.fi by bedrock.ccl.net (8.7.5/950822.1) id DAA05874; Wed, 11 Sep 1996 03:49:48 -0400 (EDT) Received: from phcu.helsinki.fi by phcu.helsinki.fi (PMDF V5.0-4 #1) id <01I9CI8JDKCW9BVD8S@phcu.helsinki.fi> for chemistry@ccl.net; Wed, 11 Sep 1996 10:49:47 +0300 Date: Wed, 11 Sep 1996 10:32:18 +0300 From: Tom Sundius U of Helsinki +358 0 1918339 Subject: Re: CCL:Wilson Out-Of-Plane Coordinate In-reply-to: "Your message dated Tue, 10 Sep 1996 16:29:26 -0600" <9609101629.ZM8789@indi.aci.uni-heidelberg.de> To: chemistry@ccl.net Message-id: <01I9CLTTJ2Y29BVD8S@phcu.helsinki.fi> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT > Could someone explain me what exactly the Wilson out-of-plane > coordinate is? ... > I have the corresponding reference > Wilson, E. B.; Decius, J. C.; Cross, P. C. Molecular Vibrations, > Dover, New York (1980). > but we don't have the book here. Another reference, which may be very helpful, is S. Califano: Vibrational States, J. Wiley & Sons, London (1976) ISBN 0-471-12996-8 (there may be a new edition of this useful book) Chapter 4 of this book deals with the Wilson internal coordinates. Sometimes the out-plane bend coordinate is also defined as "impromper torsion" which involves the dihedral angle between two adjoining planes. The difference between the two definitions is, however, insignificant for an (almost) planar configuration. +-----------------------------------------------------------------------+ ! Tom Sundius, Dept. of Physics Internet: Tom.Sundius@Helsinki.fi ! ! University of Helsinki, Finland sundius@phcu.helsinki.fi ! +-----------------------------------------------------------------------+ From Tanaka_Toshimasa@takeda.co.jp Wed Sep 11 06:10:56 1996 Received: from ineto.takeda.co.jp for Tanaka_Toshimasa@takeda.co.jp by www.ccl.net (8.7.5/950822.1) id FAA07195; Wed, 11 Sep 1996 05:37:28 -0400 (EDT) From: Received: from inetmi.inet.takeda.co.jp by ineto.takeda.co.jp (8.6.12+2.5W/4.03) id SAA14958; Wed, 11 Sep 1996 18:32:11 +0900 Received: from ineti.inet.takeda.co.jp by inetmi.inet.takeda.co.jp (8.6.12+2.5W/4.03) id SAA16491; Wed, 11 Sep 1996 18:32:02 +0900 Received: from po_osaka by ineti.inet.takeda.co.jp (8.6.12+2.5W/4.03) id SAA17596; Wed, 11 Sep 1996 18:33:03 +0900 Received: from by takeda.co.jp with SMTP (1.38.193.5/16.2) id AA18509; Wed, 11 Sep 1996 18:39:03 +0900 X-Openmail-Hops: 1 Date: Wed, 11 Sep 96 18:38:35 +0900 Message-Id: Subject: SUMMARY: PostScript Mime-Version: 1.0 To: chemistry@www.ccl.net Content-Type: multipart/alternative; boundary=openmail-part-01740b45-00000002 --openmail-part-01740b45-00000002 Content-Type:text/plain; charset=ISO-2022-JP Dear netters, a week ago, I posted a question regarding software that convert a PostScript file into a Macintosh file. I thank many CCLers who responded to my request. My original question was that (IR(JDoes anyone know of a free or shareware that can convert a SGI postscript file to a macintosh postscript one?(IS(J. As pointed out by some people, there is only one PostScript (if the difference level 1 and level 2 is ignored). So it should have been exactly as (IR(JDoes anyone ... convert a PostScript file into a EPS(Encapsulated PostScript) file for Macintosh. What I wanted to try are 1) adding(by overwriting or editting) some characters and pictures on PostSctipt images, which were moved to Mac from SGI workstation, using an application such as Word, ChemDraw,etc.... and 2) getting good outputs of them trough a PostScript Printer. There is a short summary of responses focasing on softwares. ---------------------------------------------------------------------------- *PS2EPS+ (Macintosh freeware written by Peter Lerup) can generate visible picture(screen preview) from PostScript files. The primary usage of this program is to genarate EPS files from plain PS text files. This is act as a front program of Ghoastscript [http:search.shareware.com] .....I tried to convert a PostScript file into EPS by PS2EPS+ and imported it into Word and ChemDraw Pro. Next, I overwrote some pictures on it using painting tools in Word and sent it to a printer, then a PostScript printer gave a fine output. I wonder if this is a kind of easiest methods to modify PostScript files. In case of ChemDraw, however, I could not obtain a good result...... *GSViewer (Macintosh freeware written by Mark Lentcznek) is also a front program of Ghostscript. This software can display PostScript files by screen preview,send it to a printer and save it as a PICT file. [http://ftp.cs.wisc.edu/pub/ghost/aladdin/mac] *DropPS (macintosh freeware written by Rich Siegel) is a utility to send PostScript files (without creating screen previews) to any PostScript printer connected to an AppleTalk network. [http://hyperarchive.lcs.mit.edu/HyperArchive.html] *XTRA for Macintosh FreeHand is a third-party program that supposedly allows one to import a PostScript file and edit it.You(IU(Jd have to buy Macromind FreeHand and TechPool XTRA. [http://www.macromedia.com/software/xtras/freehand/techpool.html] *GraphicConverter (Macintosh shareware written by Thorsten Lemke) converts pictures of different formats and has a number of useful picture-handling features. The new version of it(V2.4.3) can read EPS files if you(IU(Jve got a shareware called EPStoPICT and registered it. .....GraphicConverter can read EPS files, which were converted from PostScript files by PS2EPS+, as PICT..... This can convert very lots of kinds formats including SGI image (.rgb file). [http://search.shareware.com] *epsConverter (Macintosh shareware written by Sam Weiss) can read any portable EPS files and convert it into Adobe Illustrator EPS files. .....I have no Adobe Illustrator, so I cannot try it. ..... [http://search.shareware.com] ---------------------------------------------------------------------------- *pstops (a unix program, copyright to Angus J. C. Duggan) is one of the softwares called (IR(JPS utility package(IS(J. This is used like an unix command containing no viewer. [NetSearch; Excite Serch etc.] *tops (IRIX command) converts iris image to PostScript. Example; %tops (file name.rgb) -eps > (file name.eps) ---------------------------------------------------------------------------- *pgdraw (Windows freeware) can edit PostScript files. ATM(Adobe Type Manager) is necessary to annotate by pgdraw. [http://search.shareware.com] ---------------------------------------------------------------------------- Best regards, Toshimasa Tanaka xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Toshimasa TANAKA Molecular Chemistry Laboratory Pharmaceutical Research Division Takeda Chemical Industries, LTD. E-Mail Tanaka_Toshimasa@takeda.co.jp xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --openmail-part-01740b45-00000002 Content-Type:text/plain; charset=ISO-2022-JP --openmail-part-01740b45-00000002-- From owner-chemistry@ccl.net Wed Sep 11 06:22:28 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id FAA07232; Wed, 11 Sep 1996 05:54:42 -0400 (EDT) Received: from goliat.ugr.es for aentrena@goliat.ugr.es by bedrock.ccl.net (8.7.5/950822.1) id FAA06260; Wed, 11 Sep 1996 05:54:39 -0400 (EDT) Received: from quimfarm2 (quimfarm2.ugr.es [150.214.65.52]) by goliat.ugr.es (8.6.10/8.6.12) with SMTP id LAA02976 for ; Wed, 11 Sep 1996 11:58:45 +0100 Message-ID: <323706A8.2C0@goliat.ugr.es> Date: Wed, 11 Sep 1996 11:36:24 -0700 From: "Dr. Antonio Entrena" Organization: Dpto. Quimica Organica. Fac. Farmacia. Universidad de Granada. 18071 GRANADA (sPAIN) X-Mailer: Mozilla 2.0 (Win16; I) MIME-Version: 1.0 To: Computational Chemistry List Subject: TS on a SN2 reaction Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dears CCL users: Last week I post a question regarding to a TS on a SN2 reaction. I have received some responses and here is the summary: My original question was: ********************************** I need to calculate the TS for a variety of SN2 reactions using semiempirical Mopac calculation and I have some problems. I will be very greatfull for every help that you can gave me. The strategy that I have used is the following: I have define a dummy atom in order to fix the geometry of the nuclephile and the leaving group as in the following scheme: Du..........C | | Nu..........C---L I have defined the distance between the dummy atom (Du) and the upper carbon atom about 10 A and between the nucleophile (Nu) and the lower carbon atom about 5 A. The Du-C-C-Nu and Du-C-C-L dihedral angles have been defined as 0 and 180 degrees, respectively. I used the symmetry keyword (option 17) in order to varies the C-C-Nu bond angle as 180 degrees - C-C-L bond angle during the calculation. I believe that with those definitions, the nucleophile, the carbon atom and the leaving group (L) must be in straight line when the distances Nu-C is decreased at 0.1 or 0.05 A intervale. I expect that when the nucleophile is located at a apropiate distance the distance C-L begin to increase so that the geometry of higher energy could be used to optimized the TS of the reaction, but this does not occur. When the nuclephile is about 2.4-2.2 A, the leaving group is inmediately ejected to a distance of 3.5 A or more. Can anybody with experience in this type of calculations gave me some orientations to resolve this problem?. Please, e-mail directly to me and I will summarized to the net. Sincerely A. Entrena ************************************** And the answers are the following: ********************************************* From: ansu@trout.csb.ki.se (Ansuman Lahiri) Dear Dr. Entrena Did you try the SADDLE keyword in mopac? What I usually do is to choose two configurations (in one of which the leaving group is bonded and in the other the attacking group is bonded to the central group) and then run SADDLE. The approximate transition state obtained from SADDLE can then be further refined using TS. Hope this helps Good luck! Ansuman ***************************************** From: "Anatoli Korkin" Hi! Fixing C-Nu eagual C-L in optimization, you will approach TS closely. Then compute frequencies and use the resulting force field along with opt=ts option. But I have feeling, that you guy hardly undertand what are you doing and why. regards, Anatoli Korkin ******************************************************** From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) --- You wrote: I expect that when the nucleophile is located at a apropiate distance the distance C-L begin to increase so that the geometry of higher energy could be used to optimized the TS of the reaction, but this does not occur. When the nuclephile is about 2.4-2.2 A, the leaving group is inmediately ejected to a distance of 3.5 A or more. --- end of quoted material --- I am not sure what Nu/L combinations you are using, but this may be reasonable behavior. First, if either of the reactants or products are charged, then electrostatic interactions (ion-dipole) will be very strong and a true transition state may not even exist. Consider chloride attacking methyl chloride (degenerate rxn): as chloride approaches the energy falls (favorable ion-dipole interaction), then sharply rises to give a symmetric TS, then falls again to give the product ion-dipole complex. The AM1 transition state is only a kcal/mol or two higher than the separated reactants. Now consider hydroxide attacking methyl chloride: as hydroxide approaches the energy falls steadily without intervention of a transition state. This reaction is very exothermic, and bond energy changes plus electrostatic interactions erase the transition state. To summarize: 1) you may have trouble locating transition states, 2) minima may correspond to ion-dipole complexes in which reactants approach to within LESS than the sum of the nonbonded radii, 3) TS, when they do exist, should be viewed as resonance hybrids of the reactants and products, and therefore reasonably short CN and CL bond distances are expected. Finally, least motion paths are interesting, but may not tell the full story. For example, hydroxide attack on methyl chloride initially gives an ion-dipole complex in which the chloride is close to the methyl hydrogens of methanol. This is probably not the global minimum, and may not even be a local minimum. The best structure is probably one in which a hydrogen bond, Cl..HOCH3, holds the ion and dipole together. Alan Shusterman Department of Chemistry Reed College 3203 SE Woodstock Blvd Portland, OR 97202 ************************************ From: Hens Borkent Dear Dr. Entrena, There is no reason why the leaving group should stay in the neighbourhood of the carbon atom; once you're over the 'top' (TS), the structure will minimize the C-L distance. And moreover, there is no reason why the N-C-L angle should be 180 degrees, unless your carbon skeleton is symmetrical (methyl, t-butyl). The savest thing would be to do a grid search, in which you vary the C-N distance in the range 2.0 2.8, and the C-L distance something similar, depending on the nature of the leaving group. In this way you fix both values and a saddle point should appear in the grid. This point should be optimized using the TS keyword. Have a look at: http://www.caos.kun.nl/tutorials/camm/mopac/gsm.html Sincerely, -- ***** J.H. (Hens) Borkent, CAOS/CAMM Center, *CAOS * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CAMM* e-mail: borkent@caos.kun.nl ***** http://www.caos.kun.nl/staff/borkent.html **************************************************** From: Jose Ignacio Garcia He leido tu pregunta en la CCL. Puede haber varios motivos para el comporta- miento que describes. En primer lugar, la forma de la superficie de energia potencial depente por supuesto de la reaccion, de forma que podria suceder que en la reaccion particular que estas estudiando, haya una zona en la que el sistema evolucione muy rapidamente. La solucion en este caso es estudiar mas en detalle dicha region, modificando la distancia de ataque Nu-C con intervalos mas cortos. Algo parecido sucede cuando se comparan las reacciones Cl(-) + CH3Cl --> ClCH3 + Cl(-) y F(-) + CH3Cl --> FCH3 + Cl(-) En el primer caso, se obtiene un diagrama de reaccion "de libro", pero en el segundo, dependiendo de la geometria inicial y el intervalo utilizado puede obtenerse un diagrama en el que aparentemente la energia disminuye siempre, sin que aparezca barrera de activacion. Resulta necesario estudiar muy en detalle la region critica para localizar dicha barrera. Por otra parte, creo que utilizas demasiadas restricciones en el acercamiento de Nu, lo cual puede dar problemas. Ten en cuenta que cuantas mas restricciones utilices, menos representativa sera la superficie de energia calculada con respecto a la "verdadera". Nosotros solemos emplear el siguiente esquema: Nu ------C-------L Donde el diedro se fija en 180 grados y los angulos | Nu-C-Du y Du-C-L se fijan en 90 grados. Es estricta | logica, no deberia fijarse ninguna restriccion, pero Du si Nu o L llevan carga neta, la tendencia a dar reacciones "exoticas", como arrancar un proton cercano es bastante grande. Con las restricciones indicadas, se fuerza a que el ataque de Nu y la salida de L se produzcan a lo largo de una linea recta, como usualmente se asume en las SN2. Espero que estas observaciones te sean de alguna ayuda. Un cordial saludo. Jose Ignacio -- -------------------------------------------------------------------------------- Dr. Jose Ignacio Garcia-Laureiro Phone : 34-(9)76-762077 Departamento de Quimica Organica 761210 Instituto de Ciencia de Materiales de Aragon Fax : 34-(9)76-761159 C.S.I.C.-Universidad de Zaragoza e-mail: jig@qorg.unizar.es E-50009 ZARAGOZA (SPAIN) jig@msf.unizar.es jig@posta.unizar.es -------------------------------------------------------------------------------- "And all this science I don't understand it's just my job five days a week..." ELTON JOHN - Rocket man ------------------------------------------------------------------------- ********************************************** Thanks to all af them for their help. Sincerely A. Entrena From SHIL@dtpax2.ncifcrf.gov Wed Sep 11 10:10:59 1996 Received: from dtpax2.ncifcrf.gov for SHIL@dtpax2.ncifcrf.gov by www.ccl.net (8.7.5/950822.1) id KAA08805; Wed, 11 Sep 1996 10:09:00 -0400 (EDT) From: Date: Wed, 11 Sep 1996 10:10:28 -0400 (EDT) To: chemistry@www.ccl.net Message-Id: <960911101028.202229cc@dtpax2.ncifcrf.gov> Subject: SUMMARY: CompChem Journals Dear CCLers: Several days ago I asked the following questions: Has anyone of you compiled or seen a list of Journals which are mainly devoted to Computational Chemistry and/or Drug Design? Are the any web sites where I can find this? Related information such as citation rate would be helpful. Thanks. I got some replies which are summarized here. They were very helpful. Thanks to those who replied. -Leming Shi shil@dtpax2.ncifcrf.gov =============== Begin of Summary: CompChem Journals =========== ----------------- From: jeilers@daisy.ac.siue.edu (Jim Eilers) Try http://www.awod.com/netsci/ and leads from there. ----------------- From: "Thomas A Adler" I found a list of journals at the following site: http://midway.ca.sandia.gov/~mecolv/intro/intro.html ------------------- From: Konrad Hinsen Those that have Web sites are listed in http://lacebark.ntu.edu.au/chem_ref.html ------------------- From: "Lisa M. Balbes" There are some listed on my web page, http://www.cris.com/~balbes/science.html. There is a link there to Network Science, which has an extensive live of other journals. Good Luck. ------------------- From: Gerd Thys Sounds like a commercial but please try my compilation: http://sch-www.uia.ac.be/u/thys/chem.html In the section 'Journals'... I think it's a nice starting point to other places too... ------------------- From: "Dr. Neil E. Hoare" Several journals have web-sites. The following are some of the modelling oriented ones. J. Comp-Aid Mol. Des. http://wucmd.wustl.edu/jcamd/jcamd.html J. Mol. Modelling http://derioc1.organik.uni-erlangen.de/info/JMOLMOD/jmolinfo.html The J.Comp Chem also has a site. (can't find the URL !) ------------------- From: James Crabbe The journal Computers and Chemistry (Elsevier Science) has such articles. You could request a copy from d.barry@elsevier.co.uk, or view the web at : http://www.elsevier.nl:80/catalogue/SAA/205/06000/06005/379/379.html ------------------- From: Jean-marie Teuler I have tried to keep a list of chemistry related journals on our Web server http://www.cpma.u-psud.fr/revues.html ------------------- From: Arthur Wang My favorate on-line journal concerning with drug design is NetSci, which locates at: http://www.awod.com/netsci/. ------------------- From: Carlo Nervi On this URL: http://lem.ch.unito.it/chem_journals.html I maintain a list of journals, books, and others, related to chemistry. I'll be grateful, also, to anybody will give us further links. Thanx, ------------------- From: "Alexander Hillisch" Hallo CCLers! An extensive list of available online journals dealing with Biology/Biochemistry/Chemistry/Comp.Chem/Bioinformatics can be found at: http://www.imb-jena.de/journals.html The first link on this page points to: http://golgi.harvard.edu/journals.html ...another interesting list of journals. ------------------- From: "Dong Xu" I have a list of journals which cover computational biology/chemistry at http://illinois.ncifcrf.gov:1234/proteins/journal.html ------------------- ======================= END OF SUMMARY: CompChem Journals ============ From elewars@alchemy.chem.utoronto.ca Wed Sep 11 16:11:05 1996 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.7.5/950822.1) id PAA10902; Wed, 11 Sep 1996 15:29:52 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id PAA12960 for chemistry@www.ccl.net; Wed, 11 Sep 1996 15:29:49 -0400 (EDT) Date: Wed, 11 Sep 1996 15:29:49 -0400 (EDT) From: "E. Lewars" Message-Id: <199609111929.PAA12960@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: FLUXIONAL MOLECULES 1996 Sept 11 hassler@ftug01.dnet.tu-graz.ac.at asked about conformational isomerism and IR/NMR. Hdere's my $0.01 worth. Hello, Sorry if I can't contribute too much to the solution of your problems, but I have two comments: (1) Fluxional molecules are systems like cycloheptatriene/norcaradiene, or bullvalene. The term fluxional is usually applied to molecules that participate in *valence tautomerism*, not to conformationally mobile molecules (of course, almost all molecules are conformationally mobile). (2) You say "Two conformers are...not distinguishable on the time scale of IR and Ra spectroscopy." In *NMR* spectroscopy it is common for conformationally mobile species to show at room temp. only an average set of NMR signals, but to display on cooling the peaks of the individual conformers. However, so far as I know the frequency of IR radiation is so much higher than that of radio waves that IR/Raman spectroscopy always takes snapshots of the individual conformers. The freq of rotation about single bonds is about 10**12 Hz (ca. 100 cm**-1), while IR radiation has a freq of ca. 10**13 Hz (ca. 1000 cm**-1). So IR does not see the individual conformers as a blur. For example, the IR of butane is a superimposition of the IR's of the gauche and anti conformers. Ich denke, Sie mu:ssen eine a:usserst niedrige Barrierre haben, wenn es nicht mo:glich ist, die individuelle Konformationen zu unterscheiden. === Errol Lewars ==== >Subject: CCL:fluxious molecules >Sender: Computational Chemistry List >To: FULTRX"chemistry@ccl.net"@ccl.net >Dear members of CCL! >I have two questions concerning vibrational spectroscopy (IR,Ra) of fluxious >molecules. >Problem 1: the conformers are not distinguishable on the time scale of IR and Ra >spectroscopy. ====================== From owner-chemistry@ccl.net Wed Sep 11 18:11:05 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id RAA11793; Wed, 11 Sep 1996 17:48:38 -0400 (EDT) Received: from copland.udel.edu for sbennett@wotan.duch.udel.edu by bedrock.ccl.net (8.7.5/950822.1) id RAA24782; Wed, 11 Sep 1996 17:48:37 -0400 (EDT) Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by copland.udel.edu (8.7.5/8.7.3) with SMTP id RAA15414 for <@brahms.udel.edu:chemistry@ccl.net>; Wed, 11 Sep 1996 17:48:38 -0400 (EDT) Received: by wotan.duch.udel.edu (940816.SGI.8.6.9/930416.SGI) id RAA03229; Wed, 11 Sep 1996 17:42:17 -0400 Date: Wed, 11 Sep 1996 17:42:17 -0400 (EDT) From: Steve Bennett To: CCL Users Subject: Polarizablities Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We are looking for a program (or even better source code) of a program that calculates polarizabilities of molecules. I am familiar with an old (1976) empirical method devised by Miller and Savchik (JACS 101, 7206) but would like a more recent program adaptable to organometallic species, in addition to organics. Thanks in advance. Results will be compiled and reposted. Steven D. Bennett University of Delaware Department of Chemistry 304A Drake Hall (302) 831-8720 sbennett@wotan.duch.udel.edu (302) 737-8485 http://www.udel.edu/arcade/steves.html "Although the answer is not unknown, I'm searchin', searchin, and how I've grown; It's not all right to say goodbye, and the world on a string doesn't mean a thing" Neil Young From leclerf@MEDCN.UMontreal.CA Wed Sep 11 19:11:05 1996 Received: from condor.CC.UMontreal.CA for leclerf@MEDCN.UMontreal.CA by www.ccl.net (8.7.5/950822.1) id SAA12038; Wed, 11 Sep 1996 18:43:58 -0400 (EDT) Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by condor.CC.UMontreal.CA with ESMTP id WAA24609 (8.6.11/IDA-1.6 for ); Wed, 11 Sep 1996 22:41:51 GMT Received: from med07.MEDCN.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id SAA01777; Wed, 11 Sep 1996 18:44:26 -0400 Received: by med07.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id SAA27265; Wed, 11 Sep 1996 18:44:25 -0400 Date: Wed, 11 Sep 1996 18:44:25 -0400 From: leclerf@MEDCN.UMontreal.CA (Leclerc Fabrice) Message-Id: <9609111844.ZM27261@med07.MEDCN.UMontreal.CA> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: homology modeling Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.19609111844.ZM27261.MEDCN.UMontreal.CA" --PART-BOUNDARY=.19609111844.ZM27261.MEDCN.UMontreal.CA Content-Description: Text Content-Type: text/plain ; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Zm-Decoding-Hint: mimencode -q -u Hello, I'm looking for examples of homology modeling methods validated by the comparison between the model built and the known structure determined by = X-ray crystallography. Any reference about such examples ? Thanks. -- = \ /\ \/ \______________________________________ /\ = A--T Fabrice Leclerc = (----) D=E9partement de Biochimie G--C Universit=E9 de Montr=E9al = \/ C.P. 6128, succ. Centre-Ville = /\ Montr=E9al, Qu=E9bec H3C 3J7 = T--A Canada (----) t=E9l. +1 (514)343-6111 poste 5354 C--G fax. +1 (514)343-2177 \/ leclerf@MEDCN.UMontreal.CA /\ _____________________________________ / \ / \/ --PART-BOUNDARY=.19609111844.ZM27261.MEDCN.UMontreal.CA-- From owner-chemistry@ccl.net Wed Sep 11 20:11:06 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id TAA12171; Wed, 11 Sep 1996 19:24:28 -0400 (EDT) Received: from kodakr.kodak.com for lrbu00@xd88.kodak.com by bedrock.ccl.net (8.7.5/950822.1) id TAA25735; Wed, 11 Sep 1996 19:24:28 -0400 (EDT) From: Received: from euler.kodak.com by kodakr.kodak.com with SMTP id AA28288 (5.67b/IDA-1.5 for <@kodakr.kodak.com:chemistry@ccl.net>); Wed, 11 Sep 1996 15:37:01 -0400 Received: from xd88.kodak.com by euler.kodak.com via SMTP (940816.SGI.8.6.9/940406.SGI) for id PAA01219; Wed, 11 Sep 1996 15:37:08 -0400 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA15928; Wed, 11 Sep 1996 15:37:07 -0400 Date: Wed, 11 Sep 1996 15:37:07 -0400 Message-Id: <9609111537.ZM9782@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: chemistry@ccl.net Subject: Hewlett-Packard Printers and Unix Boxes Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Netters: Has anyone had any success using an HP printyer that was directly attached to a Unix box? If so where were any requisite drivers found? Will post results. Thanks, John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From amasunov@email.gc.cuny.edu Wed Sep 11 22:11:07 1996 Received: from gaudi.gc.cuny.edu for amasunov@email.gc.cuny.edu by www.ccl.net (8.7.5/950822.1) id WAA12769; Wed, 11 Sep 1996 22:06:40 -0400 (EDT) Received: from broadway.gc.cuny.edu (broadway.gc.cuny.edu) by GAUDI.GC.CUNY.EDU (PMDF V5.0-5 #13310) id <01I9D9GYTHLC0015GN@GAUDI.GC.CUNY.EDU> for chemistry@www.ccl.net; Wed, 11 Sep 1996 22:06:37 -0400 (EDT) Received: from localhost (amasunov@localhost) by broadway.gc.cuny.edu (8.7.5/ank-osf96) with SMTP id WAA22763 for ; Wed, 11 Sep 1996 22:06:36 -0400 (EDT) Date: Wed, 11 Sep 1996 22:06:36 -0400 (EDT) From: Artem Masunov Subject: RE: Summary on molecular crystals X-Sender: amasunov@broadway.gc.cuny.edu To: CCL Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT > I'm looking for a summary on the packing of organic molecular crystals. > I know some papers from Kitaigorodskii about the subject but haven't > found a summary. +---------------------------------------------------------------------+ | Stefan Reichling | | Anorganisch-Chemisches Instiut | | Tel +49-6221-548649 Universitaet Heidelberg | | Fax +49-6221-545707 69120 Heidelberg | | e-mail: steve@indi.aci.uni-heidelberg.de Germany | | www: http://ix.urz.uni-heidelberg.de/~il1 | www: http://ix.urz.uni-heidelberg.de/~il1 | +---------------------------------------------------------------------+ Dear Steve, It is pretty broad area you are going into. If you are looking for the summary of Kitaigorodskii's papers, see his books "Molecular Crystals" and "Mixed Crystals". Both are available in English edition. Among more recent books you might be interested in "Molecular Crystals" by Willis and "Crystal Engineering" by Desiraju. Wast reviews were also published (separately) by Gavezzotti, Bernstein, Leizerovitz, Brock, Murray-Rust and some others. We did some generalizations on biphenyls and uracils, too: Russ.J.Phys.Chem. 1992, 66(1) 23-30; Russ.J.Phys.Chem. 1993, 67(2) 201-217. More complete list could be obtained from Cambridge Crystallographyic Database (DBUSE subset). If you need more details or I misspelled any name above, please do not hesitate to contact me. Regards, Artem > __ _________ > / \ / _ _ \ Artem Masunov - amasunov@shiva.hunter.cuny.edu > / \\ \\ \\ \ Chemistry Department, Hunter College > / /\ \\ \\ \\ \ City University of New York > / ____ \\ \\ \\ \ 695 Park Avenue, New York, NY 10021 > /__/\__/\__\\__\\__\\__\ Tel: (212) 772-5751, Fax: (212) 772-5332 > \__\/ \/__//__//__//__/ Bpr: 91-777-333-91, that is (917) 773-3391 > > I know you believe you understand what you think I said, but I am not > sure you realize that what you heard is not what I meant. (Gaussian92)