From chemistry-request@server.ccl.net Wed Oct 6 06:52:48 1999 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA27204 for ; Wed, 6 Oct 1999 06:52:46 -0400 Received: from npd.ufpe.br (Rlongo2.DQF.UFPE.BR) by npd.ufpe.br (PMDF V5.1-4 #20469) with ESMTP id <01JGT3T72DE8000BNV@npd.ufpe.br> for chemistry@ccl.net; Wed, 6 Oct 1999 08:43:37 GMT-3 Date: Wed, 06 Oct 1999 08:46:37 -0300 From: Marcelo Zaldini Hernandes Subject: au on G94W output To: chemistry@ccl.net Message-id: <37FB369D.652D9442@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (Win98; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear Colleagues, Does anybody know how to select atomic units (bohr) on G94W outputs ? The keyword units=au just select "input" atomic units. There is some IOP comand to do this ? Thanks in advance. -- ************************************** Marcelo Zaldini Hernandes ************************************** From chemistry-request@server.ccl.net Tue Oct 5 18:19:42 1999 Received: from mgcct6.nci.nih.gov (mgcct6.nci.nih.gov [137.187.211.216]) by server.ccl.net (8.8.7/8.8.7) with SMTP id SAA22917 for ; Tue, 5 Oct 1999 18:19:42 -0400 Received: from helix.nih.gov (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id UAA11064; Tue, 5 Oct 1999 20:09:13 -0400 Sender: brunob@helix.nih.gov Message-ID: <37FA9329.3BCAC017@helix.nih.gov> Date: Tue, 05 Oct 1999 20:09:13 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 4.6 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Computer Chemistry List CC: Marc Zimmer Subject: Summary: Automatic docking with Macromodel Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id SAA22918 Dear CCL, One week ago I posted : " I am interested in automatic docking of small molecules to a protein using a program equipped with a non explicit solvent model. I plan to use the MMFF with the GB/SA water solvation model as implemented in Macromodel 6.5 for this task. I also would like selected residues of the binding site to be flexible whereas the rest of the receptor would be fixed. According to the user's manual pages 75 and 77, the MOLS option of the MC, SD and MD related commands can be used for docking searches. Unfortunately, I haven't found examples or pratical recipes to perform automatic docking this way. Could someone provide me pointers (references, recipes, examples)? " Thanks to Marc Zimmer who wrote: We have used the MOLS command within a MC search to dock luciferin into luciferase. "Site-Directed Mutagenesis of Histidine 245 in Firefly Luciferase: A proposed Model for the Active Site" B. Branchini, R. Magyar, M. Murtiashaw, S. Anderson*, M. Zimmer, Biochemistry 1998,37, 15311. -- [ Bruno Bienfait, Ph. D. Laboratory of Medicinal Chemistry ] [ National Cancer Institute ] [ Email : brunob@helix.nih.gov National Institutes of Health ] [ Phone : (301) 402-3111 Building 37, Room 5B20 ] [ Fax : (301) 496-5839 Bethesda Maryland 20892 , USA ] [ WWW : http://www.brunob.org ] From chemistry-request@server.ccl.net Tue Oct 5 21:27:43 1999 Received: from yakko.cimav.edu.mx ([207.248.161.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA24289 for ; Tue, 5 Oct 1999 21:27:42 -0400 Received: from localhost (glossman@localhost) by yakko.cimav.edu.mx (8.8.7/8.8.7) with ESMTP id TAA20026 for ; Tue, 5 Oct 1999 19:19:42 -0500 Date: Tue, 5 Oct 1999 19:19:42 -0500 (CDT) From: Daniel Glossman To: CHEMISTRY@ccl.net Subject: carbon black-polymer composites Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: Can somebody point me to bibliographic information, published results or WEB pages related to the computational chemistry and/or molecular modeling of carbon black-polymer composites? Thanks in advance Dr. Daniel Glossman ************************************************************************** * Dr. Daniel Glossman * Phone: (52) 1 4391151 * * Centro de Investigacion en * FAX: (52) 1 4391112 * * Materiales Avanzados (CIMAV) * E-mail: glossman@mail.cimav.edu.mx * * Departamento de Polimeros * glossman@hotmail.com * * Miguel de Cervantes 120 * * * Complejo Industrial Chihuahua * * * Chihuahua, Chih. 31109 * * * Mexico * * ************************************************************************** From chemistry-request@server.ccl.net Tue Oct 5 21:35:31 1999 Received: from smtppop1.gte.net (smtppop1.gte.net [207.115.153.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA24411 for ; Tue, 5 Oct 1999 21:35:31 -0400 Received: from oemcomputer (1Cust166.tnt4.bos2.da.uu.net [63.22.97.166]) by smtppop1.gte.net with SMTP for ; id UAA3481195 Tue, 5 Oct 1999 20:20:04 -0500 (CDT) Message-ID: <000701bf0f98$ebfc7660$32b4fea9@oemcomputer> From: "David Anick" To: Subject: t-state for peptide hydrolysis Date: Tue, 5 Oct 1999 21:19:52 -0400 Dear CCLers, I posted a query on the t-state for peptide bond hydrolysis. There were three responses, that were quite helpful. Thank you all very much. Here they are: 1. Hello, Mark Gordon, Kim, Baldridge and I have a published a paper on the subject in J. Phys. Chem. sometime in the early nineties. Best regards, Jan Jensen Assistant Professor of Chemistry University of Iowa [NOTE: The reference is: Jan H. Jensen, Kim H. Baldridge, and Mark S. Gordon, Uncatalyzed Peptide Bond Formation in the Gas Phase, J. Phys. Chem. 96 (1992), 8340-8351.] 2. [Sent by Matthew Schlecht:] Dave, I don't know if it contains all the data you seek (I don't have the paper easily accessible), but I think the following Clark Still paper contains some of the thermodynamic values you're looking for: "Hydrolysis of a Peptide Bond in Neutral Water" Kahne, D.; Still, W. C. J. Am. Chem. Soc. 1988 110 7529. 3. Hi, David, I did some calculations on amide bond hydrolysis, which may be of interest to you. Although it is a peptide by itself, it should be close mimic. Both geometries and energetics in gas phase and solution were calculated and compared with experimental data. As for enzymatic free energy barrier, it can be calculated easily from rate constant. The reference is: J. Mol. Struct. (THEOCHEM.) 1998, 429, 41-48 (A theoretical study of a nucleophilic addition reaction in the gas phase amd in aqueous solution: peptide bond hydrolysis). Hope this is useful to you. Take care. Yajun **************************************************** Ya-Jun Zheng, Ph.D DuPont Stine-Haskell Research Center P. O. Box 30 Newark, Delaware 19714 Phone: (302) 366-5231 or (302) 695-1440 Fax: (302) 366-5783 E-mail: Ya-Jun.Zheng@usa.dupont.com **************************************************** From chemistry-request@server.ccl.net Wed Oct 6 16:27:07 1999 Received: from gw.kirkwood.k12.mo.us ([204.184.190.253]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA01001 for ; Wed, 6 Oct 1999 16:27:06 -0400 Received: from KR7DOM-Message_Server by gw.kirkwood.k12.mo.us with Novell_GroupWise; Wed, 06 Oct 1999 15:30:03 -0500 Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Wed, 06 Oct 1999 15:29:24 -0500 From: "John Mackin" To: chemistry@ccl.net Subject: computational chem for high school students I am interested in any very basic applications which will help high school chemistry students appreciate the use of technology and math in the current development of chemistry. These students have algebra capability (no calculus) so the math component must be more simple than I suspect is used in computational chemistry. The graphics results, though, will spark interest in the students. Again, the key word is appreciation. Are there applications which would excite and motivate some students to pursue a chemistry career in college? From chemistry-request@server.ccl.net Tue Oct 5 12:56:27 1999 Received: from dcmail1.dowcorning.com (dcmail1.dowcorning.com [208.154.221.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA21658 for ; Tue, 5 Oct 1999 12:56:26 -0400 From: c.peter.qian@dowcorning.com Received: from dcmailfw.dowcornusa.com (unverified) by dcmail1.dowcorning.com (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Tue, 05 Oct 1999 12:28:44 -0400 Received: from corpnt83.dowcornusa.com (unverified) by dcmailfw.dowcornusa.com (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Tue, 05 Oct 1999 12:31:17 -0400 Received: by corpnt83.dowcornusa.com with Internet Mail Service (5.5.2448.0) id ; Tue, 5 Oct 1999 12:47:56 -0400 Message-Id: To: chemistry@ccl.net Subject: Software for simulating O17 NMR spectrum Date: Tue, 5 Oct 1999 12:47:44 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Dear CCL: I am interested in simulating O17 NMR spectrum for organic molecules. I appreciate if CCL members can send me information regarding O17 NMR simulation software (both PC or Unix based, commercial or academic). Thanks in advance. Peter Qian Dow Corning Corporation * Voice: (517)496-6938 Interface Expertise Center, CO41D1 * Fax: (517)496-5121 Midland, MI 48686, USA * e-mail: c.peter.qian@dowcorning.com *********************************************************** This email transmission and any files that accompany it may contain sensitive information belonging to the sender. The information is intended only for the use of the individual or entity named. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email transmission in error, please immediately notify the Security Administrator. Security.Administrator@dowcorning.com *********************************************************** From chemistry-request@server.ccl.net Wed Oct 6 02:33:04 1999 Received: from csc.contservice.ru (root@dolgop-gw.GLAS.net [195.218.178.26] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA25427 for ; Wed, 6 Oct 1999 02:32:57 -0400 Received: from AndL ([192.168.1.9]) by csc.contservice.ru (8.9.3/8.9.3) with SMTP id KAA03045 for ; Wed, 6 Oct 1999 10:16:53 +0400 Message-ID: <009901bf0fbb$00e87ac0$0901a8c0@AndL> Reply-To: "Andrey Losev" From: "Andrey Losev" To: Subject: WEB LINK Date: Wed, 6 Oct 1999 09:24:02 +0400 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1251" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear Colleague, ChemDiv, Inc., combines the expertize in small molecule "historical" compound collections with combinatorial chemistry, custom synthesis and other chemistry development services for drug discovery The complete information regarding our research products and services you can find on our www.chemdiv.com site. We arranged the set of useful links on our site promoting an access of our customers to other useful resources please find "Useful Links" page of our site. We are very intrested in exchanging links with your site, and we are ready to place a link to your site there. We would appreciate if you could place a link to our site among analogous information on your web site. We hope, that visitors of your site might be interested in our products and services as well. If any terms applied we would very much appreciate sending us the list of such terms. Thank you, Best regards, Andrey Losev Marketing Manager ChemDiv, Inc. 11575 Sorrento Valley Road, Suit 210 San Diego, CA 92121 USA Tell: (619) 794 4860 Fax: (619) 794 4931 Email:maricont@glasnet.ru chemdiv@pacbell.net From chemistry-request@server.ccl.net Tue Oct 5 10:12:39 1999 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA20966 for ; Tue, 5 Oct 1999 10:12:37 -0400 Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id QAA01156 for ; Tue, 5 Oct 1999 16:56:20 +0300 (EET DST) Date: Tue, 5 Oct 1999 16:56:20 +0300 (EET DST) From: John Kerkines To: chemistry@ccl.net Subject: MOPAC Parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Listmembers, We are trying to find MOPAC parameters for the elements W and Mo. Any help would be very much appreciated. Regards, John Kerkines Athens, Greece From chemistry-request@server.ccl.net Wed Oct 6 17:11:48 1999 Received: from mx.iki.rssi.ru (mx.iki.rssi.ru [193.232.212.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA01520 for ; Wed, 6 Oct 1999 17:11:46 -0400 Received: from mx.icp.rssi.ru (mx.icp.rssi.ru [194.85.223.7]) by mx.iki.rssi.ru (8.9.1/8.9.1) with ESMTP id BAA03257 for ; Thu, 7 Oct 1999 01:09:06 +0400 (MSD) Received: from sasha ([194.85.223.62]) by mx.icp.rssi.ru (post.office MTA v1.9.3b **** trial license expired ****) with SMTP id AAA52 for ; Thu, 7 Oct 1999 01:08:32 +0400 Reply-To: From: sasha@mx.icp.rssi.ru (Alexander Bagatur'yants) To: "CCL" Subject: Force field for silanes Date: Thu, 7 Oct 1999 01:11:53 +0400 Message-ID: <000201bf103f$699f60e0$3edf55c2@sasha> MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Dear colleagues, I am interested in force filed parameters for silanes. I will appreciate any data or references and will summarize the answers. Best wishes, Prof. Alexander Bagatur'yants Photochemistry Center, Russian Academy of Sciences ul. Novatorov 7a, Moscow, 117421 Russia Phone: (007-095)-936-2588 Fax: (007-095)-936-1255 E-mail: sasha@icp.rssi.ru Home page: http://www.icp.rssi.ru/eng/bagat/bagat.htm From chemistry-request@server.ccl.net Wed Oct 6 16:38:40 1999 Received: from carbon.foodsci.unibo.it (mac@carbon.foodsci.unibo.it [137.204.211.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA01297 for ; Wed, 6 Oct 1999 16:38:39 -0400 Received: from localhost (mac@localhost) by carbon.foodsci.unibo.it (8.9.3/8.9.3) with ESMTP id XAA14016 for ; Wed, 6 Oct 1999 23:43:08 +0200 X-Authentication-Warning: carbon.foodsci.unibo.it: mac owned process doing -bs Date: Wed, 6 Oct 1999 23:43:08 +0200 (MEST) From: Mauro Andrea Cremonini To: chemistry@ccl.net Subject: Q: programs for chemical shift calculations? In-Reply-To: <37FB369D.652D9442@npd.ufpe.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear collegues, I need to perform some 17-O chemical shifts calculations of some organic derivatives. I surfed the web, but only found very expensive commercial programs that calculate NMR shifts ab initio. I would be glad if someone could tell me whether some free (or not expensive) programs exist that perform these calculations. Thank you very much for your help. M. A. C. ============================================ Mauro Andrea Cremonini, Ph.D. Food Science and Technology Laboratory University of Bologna Via Ravennate 1020 - 47023 - Cesena - Italy Phone: +39.0547.636106 FAX: +39.0547.382348 e-mail: mac@foodsci.unibo.it ============================================