From ccl@www.ccl.net Wed Jan 8 01:14:52 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id AAA26888; Wed, 8 Jan 1997 00:30:49 -0500 (EST) Received: from uniwa.uwa.edu.au for mw@crystal.uwa.edu.au by bedrock.ccl.net (8.8.3/950822.1) id AAA05986; Wed, 8 Jan 1997 00:30:46 -0500 (EST) Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by uniwa.uwa.edu.au (8.7.5/8.7.3) with SMTP id NAA18858 for ; Wed, 8 Jan 1997 13:30:42 +0800 Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA00501; Wed, 8 Jan 1997 15:57:38 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9701080528.AA08024@pack.crystal.uwa.edu.au> Subject: KCr-Alum? To: CHEMISTRY@ccl.net Date: Wed, 8 Jan 97 13:28:52 WST Mailer: Elm [revision: 70.85] Dear All, I am looking for cell parameters and fractional coordinates for KCr(SO4)2.12H2O alum, however I need neutron diffraction results only, could someone send them to me. Thank you very much. magda (mw@crystal.uwa.edu.au) From ccl@www.ccl.net Wed Jan 8 04:14:55 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id DAA27861; Wed, 8 Jan 1997 03:19:39 -0500 (EST) Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by bedrock.ccl.net (8.8.3/950822.1) id DAA07507; Wed, 8 Jan 1997 03:18:50 -0500 (EST) Received: from judy.ic.ac.uk [155.198.5.5] by romeo.ic.ac.uk with esmtp (Exim 0.57 #1) id 0vhtDl-0006Kh-00; Wed, 8 Jan 1997 08:18:49 +0000 Received: from cscmgb.cc.ic.ac.uk (sg1.cc.ic.ac.uk [155.198.63.8]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id IAA24189 for ; Wed, 8 Jan 1997 08:18:45 GMT Received: from [155.198.224.86] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id IAA01631; Wed, 8 Jan 1997 08:17:01 GMT Date: Wed, 8 Jan 1997 08:17:01 GMT X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: ANNOUNCE: CML (Chemical Markup Language) V1.0 Forwarded on behalf of Peter Murray-Rust >CML V1.0 is finally ready and posted and available for anyone who wishes >to develop applications. It's free, as are the supporting java classes, >and we are already starting to build a community of developers. > >CML V1.0 has many new features, and has vastly expanded its potential >applications. I have tackled many different disciplines and files and >believe that CML is powerful enough to represent most of them, and >certainly the chemical/* MIME types that I'm grafting through. > >The greatest enhancement is that CML is completely supported by Java >classes. It's also compatible with the latest SGML developments on the >Internet, so it represents a single universal mechanism for realising >chemical/* MIME philosophy in being able to send and receive molecules >regardless of the platform or software. It is also far easier to extend >and develop and maintain software in Java than other languages. > >I would be interested in hearing from anyone interested in adding CML to >their toolkit. It's particularly suitable for processing legacy >information, database submission and retrieval, postprocessing and >visualisation of program output, glossary development, scientific >publication, searching of semi-structured information, etc. > >CML is being offered in close collaboration with the Open Molecule >Foundation, a non-profit consortium of those interested in developing >object-oriented approaches to molecules and their interoperability. > >PeterMR > >------------------------------------------------------------------------------- >- > > > CHEMICAL MARKUP LANGUAGE (CML) V1.0 > >CML is an SGML-based approach to managing molecular information, >especially over the Inter- and Intra-networks. Version 1.0 is a major >enhancement over previous releases and is available for anyone wishing to >develop robust, Object-Oriented molecular applications. Among its >features (many of which are new): > > Object-Oriented and implemented in JAVA with hundreds of classes > > Accepts many common file types, especially chemical/* MIME > > Can process arbitrarily large files with no information loss > > Human-readable and easy to learn > > Flexible and easily extensible to many disciplines > > Supported by a communal effort, including the Open Molecule Foundation > > Ideal for postprocessing output from calculations and instruments > > Supports complex documents, including scientific publications > > Applications in protein sequence, molecular and crystal structure, >quantum > chemistry, spectra, organic molecules, publication, education > > Closely linked to the new XML/SGML developments on the Internet > > Free, including Java classes and API. > >The home page http://www.venus.co.uk/omf/index.html includes many >screenshots of the >language at work, and Java applets are also served for those with >compatible clients (For those primarily interested in general SGML >applications, there is a complete package of java classes for SGML/XML >parsing and rendering (including Shakespeare)). > >Peter Murray-Rust > > >Peter Murray-Rust (PeterMR, ) Director, Virtual School of Molecular Sciences >Pharmaceutical Sciences, Nottingham University, NG7 2RD, UK; Tel >44-115-9515100 >Fax 5110 http://www.nottingham.ac.uk/vsms/; OMF: http://www.ch.ic.ac.uk/omf/ Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ From molchano@cacr.ioc.ac.ru Wed Jan 8 11:14:57 1997 Received: from netserv2.free.net for molchano@cacr.ioc.ac.ru by www.ccl.net (8.8.3/950822.1) id KAA00131; Wed, 8 Jan 1997 10:35:07 -0500 (EST) Received: from cacr.ioc.ac.ru by netserv2.free.net (8.6.12.C2.1/8s) with ESMTP id SAA29307 for ; Wed, 8 Jan 1997 18:35:02 +0300 Received: from [193.233.3.106] by cacr.ioc.ac.ru (8.6.12.C1/7s) with SMTP id SAA01863 for ; Wed, 8 Jan 1997 18:34:58 +0300 X-NUPop-Charset: Russian Date: Wed, 8 Jan 1997 18:34:24 +0300 (BT) From: " Marina S. Molchanova" Sender: molchano@cacr.ioc.ac.ru Message-Id: <199701081834296612.molchano@cacr.ioc.ac.ru> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net Subject: new version of program Dear Netters, The latest version of SMOG 1.6 (Structural Molecular Generation) is available in the archives of Computational Chemistry List in the directory: /pub/chemistry/software/MS-DOS/SMOG on www.ccl.net server. You can get there by anonymous ftp or via the CCL home page: http://www.ccl.net/chemistry.html SMOG is a program for exhaustive, irredundant, and efficient generation of chemical isomers by their gross formula and a set of structural constraints. You just enter the summary chemical formula and it creates all possible isomers within the constraints (e.g., number of rings) which are specified. Multiatomic ready fragments ("core fragments") may be used for generation alongside with separate atoms. SMOG runs on IBM PC-compatible computers. It requires at least 640 Kb of RAM and occupies about 1 Mb of disk space (2-3 free Mb for storing the results are also desirable). The presence of a color graphics adapter (EGA/VGA) is necessary, and a mouse is highly desirable for faster work. The program is supplied with a detailed manual and on-line help. In the case of any problems, contact Marina Molchanova (Institute of Organic Chemistry, Russian Academy of Sciences) (tel) (7-095) 135-9089; (7-095) 335-2836 (fax) (7-095) 135-5328 (E-mail) mary@lexa.ru; molchano@cacr.ioc.ac.ru From ccl@www.ccl.net Wed Jan 8 13:14:59 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA00826; Wed, 8 Jan 1997 12:17:39 -0500 (EST) Received: from mdli.com for DOUGH@mdli.com by bedrock.ccl.net (8.8.3/950822.1) id MAA15491; Wed, 8 Jan 1997 12:17:36 -0500 (EST) From: Received: from puffin.mdli.com ([191.254.19.10]) by mdlgate.mdli.com with ESMTP id <17564>; Wed, 8 Jan 1997 09:04:44 -0800 Received: from jubal.mdli.com by puffin.mdli.com (8.8.2/BCH1.0) id RAA11881; Wed, 8 Jan 1997 17:13:52 GMT Received: from gimli.mdli.com by jubal.mdli.com (8.7.3/BCH1.0) id JAA02796; Wed, 8 Jan 1997 09:13:26 -0800 Received: from mdli.com by mdli.com (PMDF V5.1-5 #15780) id <01IDYR96T6E8HSL94O@mdli.com> for chemistry@ccl.net; Wed, 8 Jan 1997 09:16:45 PST Date: Wed, 8 Jan 1997 09:16:44 -0800 Subject: Spring '97 UC Extension CAMD Course To: chemistry@ccl.net Message-id: <01IDYR96T6EAHSL94O@mdli.com> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Readers in the San Francisco area will be interested in the return of the following UC Berkeley Extension course: Perspectives in Computer-Aided Molecular Design X416.2 (2 semester units in EE and Computer Science) Scientists who use computers to study and design new molecules are faced with a bewildering array of theories, techniques, and software packages. This course provides a framework to help chemists, molecular biologists, and genetic engineers understand and apply the latest techniques in computer-aided molecular design. The instructors use a case-study approach, balancing theory with applications. Lectures and discussions are combined with computing demonstrations of popular software packages for molecular design. Topics range from traditional statistical and molecular modeling studies to more recent macromolecular and 3D structural database applications. You learn about successful strategies for lead development and optimization and are encouraged to apply the techniques to problems in your own research. This course familiarizes you with the techniques and software packages in the field, so you are able to choose an appropriate method, get the most out of it, and more effectively plan for future applications in your research. Guest lecturers include Robert McDowell (Genentech), Steve Muskal (Glaxo/Wellcome- Affymax), and Phil Magee (BIOSAR). Instructor: Douglas Henry, MDL Information Systems, Inc. (dough@mdli.com) 10 evenings, Feb. 13 thru Apr. 24: Thurs., 7-10 PM (no meeting Apr. 17) San Francisco extension center - Room 16 (near Moscone at Howard) Cost: $400 (EDP 036657) For enrollment information, see p. 112 in the UC Extension Spring '97 catalog, call (510) 642-4111, or visit http://www.unex.berkeley.edu:4243 From luo96@cyberramp.net Wed Jan 8 15:14:59 1997 Received: from mailhost.cyberramp.net for luo96@cyberramp.net by www.ccl.net (8.8.3/950822.1) id PAA01694; Wed, 8 Jan 1997 15:10:51 -0500 (EST) Received: from pm5-21.cyberramp.net (pm5-21.cyberramp.net [207.158.78.149]) by mailhost.cyberramp.net (8.8.4/8.8.4/crush-0107-1827) with SMTP id OAA25237 for ; Wed, 8 Jan 1997 14:10:48 -0600 (CST) Date: Wed, 8 Jan 1997 14:10:48 -0600 (CST) Message-Id: <199701082010.OAA25237@mailhost.cyberramp.net> X-Sender: luo96@cyberramp.net (Unverified) X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: luo96@cyberramp.net (Yu-Ran Luo) Subject: Re: CCL:vitamin B6?// Bond Dossociation Energies ? Mr. H.O. Maty wrote: >Hi! Has anybody out there done computation >on derivatives of vitamin B6 (pyridoxal >phosphate)? I would appreciate your references. >Thanks, >Mary j.o. ============= >My answer: > >Sir, I can predict and show you all data if you want to know the BDEs (Bond >Dissociation Energies) in vitamin B6 and it derivatives. > > First, please draw the molecular structures you are interested in. Then >send them to me by a fax. I will give you answer by a fax ASAP. > > After you get my prediction, you will be able > >1. to clarify and understand the molecular mechanisms of chemical and > biochemical processes; >2. to find and determine the reaction center or active sites; >3. to predict the photo- and thermal stability of the species; >4. to explain and theorize organic mass spectra; >5. to estimate constants of the reaction rates and equilibriums; >6. to design new synthetic paths for the target compounds. > > Dr. Yu-Ran Luo > Molecular Energetics Consultant > 3100 Verbena Drive > Plano, TX 75075 USA > Fax: 972-509-2075 > E-Mail: luo96@cyberramp.net > From jerry@dft.chem.cuhk.edu.hk Thu Jan 9 02:15:07 1997 Received: from iris.chem.cuhk.edu.hk for jerry@dft.chem.cuhk.edu.hk by www.ccl.net (8.8.3/950822.1) id BAA04163; Thu, 9 Jan 1997 01:27:02 -0500 (EST) Received: from dft by iris.chem.cuhk.edu.hk via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for <@iris.chem.cuhk.hk:CHEMISTRY@www.ccl.net> id OAA02384; Tue, 9 Jan 1996 14:24:04 +0800 Received: by dft (950511.SGI.8.6.12.PATCH526/930416.SGI.AUTO) id OAA10289; Thu, 9 Jan 1997 14:27:27 +0800 Date: Thu, 9 Jan 1997 14:27:27 +0800 (HKT) From: Jerry C C Chan To: CHEMISTRY@www.ccl.net Subject: A1g to T1g transition of K3Co(CN)6 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Could anyone tell me where the d-d transition A1g -> T1g of K3Co(CN)6 has been calculated in the literature (whatever the level), please? Cheers, Jerry From boyd@chem.iupui.edu Thu Jan 9 17:15:12 1997 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.8.3/950822.1) id QAA10921; Thu, 9 Jan 1997 16:49:03 -0500 (EST) Received: from macgw.chem.iupui.edu (134.68.137.71) by INDYVAX.IUPUI.EDU (PMDF V5.0-5 #5862) id <01IE0LELUPW000BTGP@INDYVAX.IUPUI.EDU> for chemistry@www.ccl.net; Thu, 09 Jan 1997 16:50:36 -0500 Date: Thu, 09 Jan 1997 16:48:27 -0500 From: Boyd Subject: editors are always the last to know To: OSC CCL Message-id: X-Mailer: Mail*Link SMTP-MS 3.0.2 Content-transfer-encoding: 7BIT CCLers, I posted an announcement on CCL a couple of days ago about the release of Volume 10 of REVIEWS IN COMPUTATIONAL CHEMISTRY. Prior to posting the announcement, our publisher had informed us that the price would be the same as for Volumes 5-9, which was $110 for individual copies and $90 with a standing order. However, today I learned that our publisher (John Wiley and Sons) has set the price at $120 and is no longer offering a standing order discount. This is most unfortunate. Wiley still offers an author's discount of 25%. Hopefully, many of you will still find the books worth the new price (and in fact, the price is less than for most other book series). I'm sorry about the incorrect information posted earlier. The editors are always the last to know. Don Donald B. Boyd, Ph.D. Research Professor of Chemistry Editor, REVIEWS IN COMPUTATIONAL CHEMISTRY Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891 Facsimile 317-274-4701 Internet boyd@chem.iupui.edu REVIEWS IN COMPUTATIONAL CHEMISTRY Home Page on the World Wide Web URL http://chem.iupui.edu/~boyd/rcc.html From Jeffrey.Nauss@UC.Edu Thu Jan 9 17:58:14 1997 Received: from blues.fd1.uc.edu for Jeffrey.Nauss@UC.Edu by www.ccl.net (8.8.3/950822.1) id RAA11058; Thu, 9 Jan 1997 17:05:28 -0500 (EST) Received: from beryllium.crs.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-7 #15949) id <01IE0LU6QKJYB123D3@UCBEH.SAN.UC.EDU>; Thu, 09 Jan 1997 17:03:10 -0500 (EST) Received: by beryllium.crs.uc.edu (951211.SGI.8.6.12.PATCH1042/940406.SGI.AUTO) id RAA05452; Thu, 09 Jan 1997 17:03:31 -0500 Date: Thu, 09 Jan 1997 17:03:29 -0500 From: Jeffrey.Nauss@UC.Edu (Jeffrey L. Nauss) Subject: Removing charges for an MD simulation To: DIBUG@sunsite.icm.edu.pl, chemistry@www.ccl.net, DIBUG@sunsite.icm.edu.pl Reply-to: Jeffrey.Nauss@UC.EDU Message-id: <9701091703.ZM5450@beryllium.crs.uc.edu> Organization: Dept. Chemistry, University of Cincinnati MIME-version: 1.0 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Zm-Priority: Low One of the problems one has in MD simulations is that long runs must be performed to see anything significant, for example, and in my specific case, determination of NMR order parameters or conformational searches. Performing the run in explicit solvent with periodic boundary conditions is undoubtably the best way to perform the simulations. However, these simulations require large amounts of CPU time and disk space for the large history files. To get around these problems, people have run simulations in vacuo. This was done in the early days of MD simulations but with parameter sets that often took into account the absence of solvent. Furthermore, electrostatic screening was accomplished by using a distance dependent dielectric constant. Still, a continuing problem that I have found during an in vacuo run is the collapse of the molecule. Proteins will shrink (in terms of the radius of gyration) and side chains will fall onto the surface of the protein. Peptides often fold up into themselves. To some extent, this collapse is a result of coulmbic interactions that are not properly shielded. Ornstein's group tried to get around this problem by rendering acidic, basic, N-termini, and C-termini functional groups net neutral (JBSD vol 9, page 935 (1992)). It appeared to be somewhat successful. Has anyone tried MD simulations, particularly with small molecules like peptides and carbohydrates, with a similar approach? I am thinking perhaps of performing the simulation with the Coulombic interactions scaled down or even shut off. Of course, one must assume that the Coulombic interactions will not play a major role in the dynamics. How valid is that assumption will depend on the system studied, I would think. Comments will be appreciated. References will be even better. -- Jeff Nauss *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** From sxr224@anugpo.anu.edu.au Thu Jan 9 20:15:15 1997 Received: from anugpo.anu.edu.au for sxr224@anugpo.anu.edu.au by www.ccl.net (8.8.3/950822.1) id TAA11564; Thu, 9 Jan 1997 19:29:20 -0500 (EST) Received: from surya.anu.edu.au (surya.anu.edu.au [150.203.193.135]) by anugpo.anu.edu.au (8.8.4/8.8.3) with SMTP id LAA07120 for ; Fri, 10 Jan 1997 11:29:20 +1100 (EST) Message-Id: <199701100029.LAA07120@anugpo.anu.edu.au> Comments: Authenticated sender is From: "Shoba.Ranganathan" To: chemistry@www.ccl.net Date: Fri, 10 Jan 1997 11:05:51 +0000 Subject: CCL:AM1 proton affinities Reply-to: Shoba.Ranganathan@anu.edu.au Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Dear CCLers, Does anyone have a reference for AM1 or semi-empirical proton affinity calculations? Please reply direct to me and I will summarize if there is enough interest. Cheers, Shoba =========================================================== Dr. Shoba RANGANATHAN Computational Mol Biology & Drug Design Group Div. of Biochemistry & Mol. Biology John Curtin School of Medical Research Australian National University Tel: +616-279-8301 Canberra ACT 0200 Fax: +616-249-0415 Australia. email:Shoba.Ranganathan@anu.edu.au ===========(http://biocomp.anu.edu.au/~sra/)============== From bartberg@chem.ufl.edu Thu Jan 9 21:15:19 1997 Received: from mailey for bartberg@chem.ufl.edu by www.ccl.net (8.8.3/950822.1) id UAA11786; Thu, 9 Jan 1997 20:17:47 -0500 (EST) Received: from localhost by mailey (SMI-8.6/4.11) id RAA13365; Thu, 9 Jan 1997 17:22:33 -0500 Date: Thu, 9 Jan 1997 17:22:33 -0500 (EST) From: "Michael D. Bartberger" X-Sender: bartberg@mailey Reply-To: "Michael D. Bartberger" To: Computational Chemistry List Subject: ESP / AIM charge fits based ON DFT wavef'n? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all: I was curious as to whether anyone had considered the 'validity' of various methods of charge fitting using DFT densities, as compared to those of, say, SCF or MP2. We are investigating B3LYP in the computation of bond energies in a series of hydrofluorocarbons. We are interested in partial charges and how this relates to the BDE. As we have the DFT BDE values, I'd like to use charges based on this method as well, rather than than that of SCF or MP2. I suppose the question is, has anyone considered the use of the typical (Mulliken, ESP, or AIM-based) charge schemes with DFT densities, and / or compared them to those using SCF or MP2 values? I'd appreciate any references, personal accounts, or general sentiments about this. I'll certainly summarize. Thanks very much, -Michael ________________________________________________________________________________ Michael D. Bartberger bartberg@chem.ufl.edu TEL: (352) 392-3580 Department of Chemistry bartberg@qtp.ufl.edu FAX: (352) 846-0296 University of Florida Gainesville, FL 32611 USA ________________________________________________________________________________