From chemistry-request@server.ccl.net Mon Feb 24 10:21:53 2003 Received: from anchor-post-39.mail.demon.net ([194.217.242.80]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1OFLra22726 for ; Mon, 24 Feb 2003 10:21:53 -0500 Received: from chmqst.demon.co.uk ([158.152.83.101] helo=christian) by anchor-post-39.mail.demon.net with esmtp (Exim 3.36 #2) id 18nKQS-0005m1-0d; Mon, 24 Feb 2003 15:21:53 +0000 From: "David Livingstone" Organization: ChemQuest To: "Adel Abbas Ali Elazhary Sci. College" , chemistry@ccl.net Date: Mon, 24 Feb 2003 15:24:54 +0100 MIME-Version: 1.0 Subject: Re: CCL:Drug design and QSAR books Reply-to: davel@chmqst.demon.co.uk Message-ID: <3E5A3946.7982.1589C8E@localhost> X-Confirm-Reading-To: davel@chmqst.demon.co.uk X-pmrqc: 1 Priority: normal In-reply-to: X-mailer: Pegasus Mail for Windows (v4.02) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Hi, > > Dear ccl folks: > > I would gratly appreciate it if someone would recommend a book or > books about drug design and QSAR to read for someone who does not know > much about. Well I would recommend mine, wouldn't I ? "Data Analysis for Chemists; Application to QSAR and chemical product design" Oxford University Press,1995, ISBN 0 19 855728 0. I can e-mail a contents list if you're interested. Cheers, Dave. ------------------------------------------------------------------ D.J. Livingstone ChemQuest Delamere House, 1 Royal Crescent, Sandown. Isle of Wight UK PO36 8LZ Phone & Fax: +44 (0)1983 401793 e-mail davel@chmqst.demon.co.uk http://www.chmqst.demon.co.uk ------------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Feb 24 10:59:41 2003 Received: from deluge.umist.ac.uk ([130.88.120.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1OFxfa23827 for ; Mon, 24 Feb 2003 10:59:41 -0500 Received: from usman.ch.umist.ac.uk ([130.88.113.22] helo=usman) by deluge.umist.ac.uk with smtp (Exim 4.12) id 18nL13-0003Ij-00 for chemistry@ccl.net; Mon, 24 Feb 2003 15:59:41 +0000 From: "Michael Devereux" To: Subject: Split level B3LYP/HF calculations Date: Mon, 24 Feb 2003 16:07:07 -0000 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *18nL13-0003Ij-00*DT1dOihS8Ts* I recently received notification from a referee that split level B3LYP 6-311G(2d,p) // HF 6-31G* calculations are inappropriate for accurate electronic structure calculations. The reason given was that B3LYP optimizations give better geometries (HF was used in our work due to time constraints), but also that HF gives better electronic structure data. The first point had already been considered but does anyone know what the second could be referring to as I have never come accross this in the literature. Many thanks for your help, M Devereux, UMIST mcdi8md2@student.umist.ac.uk From chemistry-request@server.ccl.net Mon Feb 24 07:42:23 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1OCgHa17795 for ; Mon, 24 Feb 2003 07:42:19 -0500 Received: from fuyao ([202.38.82.238]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id UAA09946 for ; Mon, 24 Feb 2003 20:38:49 +0800 Message-ID: <001301c2dc01$ab97de50$1600a8c0@fuyao> From: "fuyao" To: Subject: the state problem in PCM model Date: Mon, 24 Feb 2003 20:38:43 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h1OCgNa17798 Hello,everyone, Thank you your suggestions on my previous questions.In fact I focused on the calculation on pKa value of some organic acid.I got some questions about the state involved in PCM model.Please give me some assistance.The questions followed as: 1. when we use PCM model to calculate the solvation energy, i.e. the free energy change of the reaction A (gas) ид A(solution). What is the state of A (gas)?What is the state of A (solution)?I guess 1 atm, 298K in gas and 1Mol/L,298K in solution.Right? 2.It is not possible to find a 1 mol/L DMSO solution in DMSO. So what does PCM provide us when calculating the solvation energy of DMSO in DMSO?and also water in water? 3.Does the above solvation( DMSO solution in DMSO) energy equal to the vaporization energy? i.e the free energy change of the following equation: H2O (liquid, 298K, 1atm(outside pressure)) ид H2O (1 atm(gas pressure), 298K)? 4.What is the reaction equation for the solvation energy of DMSO (the state of every species in the equation?)? Thank you very much in advance. ******************************************* Dr.Yao Fu Department of Chemistry University of Science & Technology of China Hefei, Anhui 230026,P. R. China Tel:86-551-3640051(House) 86-551-3606640(Office) Mobile:86-13855190155 Fax:86-551-3606689 E-mail: fuyao@mail.ustc.edu.cn ******************************************* From Dimitris.Agrafiotis@3dp.com Mon Feb 24 19:37:54 2003 -0500 Return-Path: Message-ID: <5FD66AAB0F19594292438D57B8664370ED17AB@mailsrv01.corp.3dp.com> From: "Agrafiotis, Dimitris" To: chemistry@ccl.net Subject: MACC Meeting on March 20 at Princeton University Date: Mon, 24 Feb 2003 19:37:51 -0500 Dear CCL members, I ask your indulgence for the broadcast nature of this meeting notice of local interest. The Mid-Atlantic Computational Chemistry (MACC) discussion group will be holding its next meeting on Thursday, March 20-th from 6-10 pm at the Kresge Auditorium (Room 120 Frick) at Princeton University. Prof. Johann Gasteiger from the University of Erlangen-Nurnberg will be speaking on "Multidimensional explorations into biochemical pathways". The meeting will start with social hour and pizza at 6 pm, followed by the seminar at 7 pm. Please RSVP by e-mail to agrafiotis@3dp.com. For more information on Prof. Gasteiger's research, please visit http://www2.chemie.uni-erlangen.de/people/Johann_Gasteiger/ . --- Dimitris K. Agrafiotis, PhD | E-mail: dimitris.agrafiotis@3dp.com 3-Dimensional Pharmaceuticals, Inc. | Tel: (610) 458-6045 665 Stockton Drive, Suite 104 | Fax: (610) 458-8249 Exton, PA 19341 | http://www.dimitris-agrafiotis.com From chemistry-request@server.ccl.net Mon Feb 24 12:20:56 2003 Received: from smtp1.server.rpi.edu ([128.113.2.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1OHKua26953 for ; Mon, 24 Feb 2003 12:20:56 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by smtp1.server.rpi.edu (8.12.7/8.12.7) with ESMTP id h1OHKp3p026290; Mon, 24 Feb 2003 12:20:52 -0500 Message-Id: <200302241720.h1OHKp3p026290@smtp1.server.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: davel@chmqst.demon.co.uk From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: azhary@ksu.edu.sa, chemistry@ccl.net X-Originating-Ip: 67.25.129.146 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Mon, 24 Feb 2003 12:20:51 EST X-Mailer: EMUmail 4.00 Subject: Re: CCL:Drug design and QSAR books X-RPI-Spam-Score: -1.8 () EMAIL_ATTRIBUTION,NOSPAM_INC,QUOTED_EMAIL_TEXT,SPAM_PHRASE_00_01 X-Scanned-By: MIMEDefang 2.28 On Mon, 24 Feb 2003 15:24:54 +0100 "David Livingstone" wrote: > Hi, > > > > > Dear ccl folks: > > > > I would gratly appreciate it if someone would recommend a book or > > books about drug design and QSAR to read for someone who does not know > > much about. > > Well I would recommend mine, wouldn't I ? "Data Analysis for > Chemists; Application to QSAR and chemical product design" Oxford > University Press,1995, ISBN 0 19 855728 0. > > I can e-mail a contents list if you're interested. > > Cheers, > > Dave. > > > Highly recommended (from one who, not too long ago, did not know much about it). Dr. N. Sukumar http://www.drugmining.com/ Visiting Scientist Rensselaer Department of Chemistry and Wadsworth Center, New York State Dept.of Health From chemistry-request@server.ccl.net Mon Feb 24 17:22:26 2003 Received: from ns1.scripps.edu ([192.42.82.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1OMMQa01569 for ; Mon, 24 Feb 2003 17:22:26 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.6/TSRI-4.1rx) with SMTP id h1OMMPV22856 for ; Mon, 24 Feb 2003 14:22:25 -0800 (PST) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 23667; Mon, 24 Feb 2003 14:14:47 -0800 (PST) Received: from hermes.scripps.edu (hermes.scripps.edu [137.131.140.49]) by relay2.scripps.edu (8.11.6/TSRI-4.2rAV) with ESMTP id h1OMMKC05473 for ; Mon, 24 Feb 2003 14:22:20 -0800 (PST) Received: from scripps.edu (jezebel [137.131.108.87]) by hermes.scripps.edu (SGI-8.9.3/8.9.3/TSRI-4.0.2h) with ESMTP id OAA65419 for ; Mon, 24 Feb 2003 14:22:19 -0800 (PST) Sender: chenlong@scripps.edu Message-ID: <3E5A9B1B.6B8B07B5@scripps.edu> Date: Mon, 24 Feb 2003 14:22:19 -0800 From: Chenglong Li Organization: The Scripps Research Institute X-Mailer: Mozilla 4.7 [en] (X11; U; SunOS 5.6 sun4u) X-Accept-Language: zh, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Fragment library Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers, Is there a good organic and/or pharmacophoric fragment library somewhere I can download? Thanks a lot, Chenlong Li