From chemistry-request@server.ccl.net Mon Jun 14 07:09:23 1999 Received: from www0w.netaddress.usa.net (www0w.netaddress.usa.net [204.68.24.52]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA10919 for ; Mon, 14 Jun 1999 07:09:22 -0400 Received: (qmail 11962 invoked by uid 60001); 14 Jun 1999 11:01:57 -0000 Message-ID: <19990614110157.11961.qmail@www0w.netaddress.usa.net> Received: from 204.68.24.52 by www0w via web-mailer(M3.2.0.17) on Mon Jun 14 11:01:57 GMT 1999 Date: 14 Jun 99 12:01:57 BST From: Kevin Kincaid To: chemistry@ccl.net Subject: Orbital Viewer for Jaguar output? X-Mailer: USANET web-mailer (M3.2.0.17) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id HAA10920 Hi All! Does anyone know of any software package that can be used to visualise the orbitals as obtained using Jaguar? Support for Linux ot WinNT platforms would be ideal. Thanks in advance, Kevin Kincaid. ____________ Kevin Kincaid chemistry.forums@usa.net Dublin City University, Ireland ____________________________________________________________________ Get free e-mail and a permanent address at http://www.netaddress.com/?N=1 From chemistry-request@server.ccl.net Tue Jun 15 06:00:05 1999 Received: from ns.dsm.nl (ns.dsm.nl [163.175.153.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA24487 for ; Tue, 15 Jun 1999 06:00:04 -0400 From: Steven.Creve@dsm-group.com Received: from dsm-fw1. (dsm-fw1.dsm.nl [163.175.153.254]) by ns.dsm.nl (8.8.6/MQT) with SMTP id MAA20604 for ; Tue, 15 Jun 1999 12:02:21 +0200 (METDST) Received: from localhost (root@localhost) by dsm-om1.dsm.nl (8.8.6/MQT) with SMTP id LAA03902 for chemistry@ccl.net;Tue, 15 Jun 1999 11:48:56 +0200 (METDST) X-OpenMail-Hops: 5 Date: Tue, 15 Jun 1999 11:50:23 +0200 X-OpenMail-Transport-Id: <03C53376621DF001/NL/400net/DSM/37662182.10DD.13F4.000> Message-Id: <"37662182.10DD.13F4.000*Creve_Steven_SJR//RESEARCH/NL/400net/DSM"@MHS> Subject: CCL:G:PCM MIME-Version: 1.0 TO: chemistry@ccl.net Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 7bit Hi all, For PCM calculations in Gaussian98, different outlying charge corrections exist. However, I don't see the difference between ICOMP=3 and ICOMP=4. Could anyone help me? Thanks in advance, Steven From chemistry-request@server.ccl.net Tue Jun 15 08:14:26 1999 Received: from phare.univ-lille2.fr (root@phare.univ-lille2.fr [193.51.138.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA25840 for ; Tue, 15 Jun 1999 08:14:24 -0400 Received: from icpl6 (icpl6.univ-lille2.fr [193.51.138.127]) by phare.univ-lille2.fr (8.8.7/8.8.7) with SMTP id OAA29903 for ; Tue, 15 Jun 1999 14:05:20 +0200 Message-ID: <003b01beb727$26019cc0$7f8a33c1@icpl6.univ-lille2.fr> Reply-To: "Philippe CHAVATTE" From: "Philippe CHAVATTE" To: "CCL" Subject: MOPAC calculations Date: Tue, 15 Jun 1999 14:03:53 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Dear CCLers, I encounter some problems with MOPAC geometry optimizations which abort because small changes in internal coordinates causing a large change in the distance between chemically-bound atoms. I would appreciate any suggestion on how to renumber the atoms. Best regards. P. CHAVATTE ----------------- Dr Philippe CHAVATTE Institut de Chimie Pharmaceutique Albert Lespagnol BP 83 59006 LILLE CEDEX FRANCE E-Mail : pchavatt@phare.univ-lille2.fr From chemistry-request@server.ccl.net Tue Jun 15 14:52:23 1999 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA00140 for ; Tue, 15 Jun 1999 14:52:18 -0400 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id PAA44451 for ; Tue, 15 Jun 1999 15:44:07 -0300 Date: Tue, 15 Jun 1999 15:44:07 -0300 (BSC) From: andre mauricio de oliveira To: Lista de discussao Quim Comp Subject: Re: CCL:CoMFA (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL's, I.m returnig Dr. David A. Winkler's reply on my question about 3D-QSAR for PC. Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil ---------- Forwarded message ---------- Date: Fri, 11 Jun 1999 11:14:58 +1000 From: "Dr. Dave Winkler" To: andre mauricio de oliveira Subject: Re: CCL:CoMFA >Hi all, > Can anyone point me any PC program to perform CoMFA analysis >(preferebly free)? > CoMFA is a patented technology owned by Tripos Associates (http://www.tripos.com) and is not available for the PC or for free. However, Graham Richards at Oxford University Centre for Molecular Sciences has developed the SoMFA method which approximates CoMFA. It runs on a PC and is available from his web site at Oxford (http://bellatrix.pcl.ox.ac.uk). Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au From chemistry-request@server.ccl.net Tue Jun 15 15:38:57 1999 Received: from mx.seanet.com (dns2.seanet.com [199.181.164.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA00869 for ; Tue, 15 Jun 1999 15:38:57 -0400 Received: from biggeek ([150.215.141.174]) by mx.seanet.com (8.9.3/Seanet-8.7.3) with SMTP id MAA24707 for ; Tue, 15 Jun 1999 12:31:09 -0700 (PDT) Message-ID: <000901beb765$a10ee380$ae8dd796@biggeek.wrq.com> From: "Mark Thompson" To: Subject: Ring discovery algorithm Date: Tue, 15 Jun 1999 12:31:08 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01BEB72A.F1D8CFA0" 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 This is a multi-part message in MIME format. ------=_NextPart_000_0006_01BEB72A.F1D8CFA0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable A few years back, someone described a nice algorithm for discovering = rings in molecular systems. If you recall this article, or just the authors, or any useful bit of = information, would you=20 please reply to me? Thanks in advance, Mark Thompson mthompson@seanet.com ------=_NextPart_000_0006_01BEB72A.F1D8CFA0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
A few years back, someone described a nice algorithm = for=20 discovering rings in molecular
systems.
 
If you recall this article, or just the authors, or = any useful=20 bit of information, would you
please reply to me?
 
Thanks in advance,
 
Mark Thompson
mthompson@seanet.com
 
 
 
------=_NextPart_000_0006_01BEB72A.F1D8CFA0-- From chemistry-request@server.ccl.net Tue Jun 15 16:25:40 1999 Received: from dali.chem.uab.edu (dali.chem.uab.edu [138.26.72.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA01661 for ; Tue, 15 Jun 1999 16:25:40 -0400 Received: from dali (localhost [127.0.0.1]) by dali.chem.uab.edu (AIX4.2/UCB 8.7/8.7) with SMTP id PAA16716; Tue, 15 Jun 1999 15:17:27 -0500 (CDT) Sender: prasad@dali.chem.uab.edu Message-ID: <3766B4D6.15FB@dali.chem.uab.edu> Date: Tue, 15 Jun 1999 15:17:26 -0500 From: "Dr. Bharatam V. Prasad" X-Mailer: Mozilla 3.0Gold (X11; I; AIX 2) MIME-Version: 1.0 To: chemistry@ccl.net Subject: DFT vs. conjugative stabilization Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, We are trying to obtain the extent of conjugation in substituted ethylenes. Our results indicate that the B3LYP method over estimate the conjugative stabilization as compared to SCF, MP2, G2 levels. Did anyone has any experience on the estimation of conjugative interactions or the resonance interactions using the DFT methods. How do they compare with the ab initio methods. Experience with nitro group is of special interest. Any pointers in this regard are highly appreciated. Prasad From chemistry-request@server.ccl.net Tue Jun 15 16:30:40 1999 Received: from mailrelay1.cc.columbia.edu (cu41754@mailrelay1.cc.columbia.edu [128.59.35.143]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA01759 for ; Tue, 15 Jun 1999 16:30:40 -0400 Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with ESMTP id QAA06947; Tue, 15 Jun 1999 16:22:52 -0400 (EDT) Received: from localhost (joerg@localhost) by still3.chem.columbia.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id QAA94255; Tue, 15 Jun 1999 16:22:52 -0400 (EDT) Date: Tue, 15 Jun 1999 16:22:52 -0400 (EDT) From: Joerg Weiser To: Mark Thompson cc: chemistry@ccl.net Subject: Re: CCL:Ring discovery algorithm In-Reply-To: <000901beb765$a10ee380$ae8dd796@biggeek.wrq.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Mark, an algorithm for the detection of the smallest set of smallest rings (SSSR) is described in weiser, holthausen, fitjer, j comput chem 1997, 18, 1264-1281 and references therein. hope it helps, joerg From chemistry-request@server.ccl.net Tue Jun 15 16:50:20 1999 Received: from serine.phr.utexas.edu (serine.phr.utexas.edu [128.83.164.59]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA02292 for ; Tue, 15 Jun 1999 16:50:19 -0400 Received: from serine.phr.utexas.edu (localhost [127.0.0.1]) by serine.phr.utexas.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id PAA85734; Tue, 15 Jun 1999 15:42:33 -0500 (CDT) Sender: balducci@serine.phr.utexas.edu Message-ID: <3766BAB8.5BA71D0A@serine.phr.utexas.edu> Date: Tue, 15 Jun 1999 15:42:32 -0500 From: Renzo Balducci Organization: University of Texas at Austin X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: Mark Thompson CC: chemistry@ccl.net Subject: Re: CCL:Ring discovery algorithm References: <000901beb765$a10ee380$ae8dd796@biggeek.wrq.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Mark Thompson wrote: > > A few years back, someone described a nice algorithm for discovering rings in molecular > systems. > > If you recall this article, or just the authors, or any useful bit of information, would you > please reply to me? > > Thanks in advance, > > Mark Thompson > mthompson@seanet.com > > > "Efficient Exact Solution of the Ring Perception Problem" R.Balducci and R.S.Pearlman, J.Chem.Inf.Comput.Sci. 1994, 34, 822-831 -- ------------------------------------------------------------------------ Renzo Balducci balducci@serine.phr.utexas.edu Research Associate & System Manager balducci@vax.phr.utexas.edu College of Pharmacy Voice: (512) 471-8509 Univ. of Texas --- Austin, TX 78712 FAX: (512) 471-7474 ------------------------------------------------------------------------ "We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation." Gay-Lussac (1808) ++++ stop the execution of Mumia Abu-Jamal ++++ ++++ if you agree copy these 3 sentences in your own sig ++++ ++++ see: http://www.xs4all.nl/~tank/spg-l/sigaction.htm ++++ From chemistry-request@server.ccl.net Tue Jun 15 20:52:57 1999 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA04344 for ; Tue, 15 Jun 1999 20:52:57 -0400 Received: (from huixiao@localhost) by helix.nih.gov (8.9.1a/8.9.1) id UAA2496885; Tue, 15 Jun 1999 20:45:06 -0400 (EDT) Date: Tue, 15 Jun 1999 20:45:05 -0400 From: Huixiao Hong To: Mark Thompson cc: chemistry@ccl.net Subject: Re: CCL:Ring discovery algorithm In-Reply-To: <000901beb765$a10ee380$ae8dd796@biggeek.wrq.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 15 Jun 1999, Mark Thompson wrote: > A few years back, someone described a nice algorithm for discovering rings in molecular > systems. > > If you recall this article, or just the authors, or any useful bit of information, would you > please reply to me? > > Thanks in advance, > > Mark Thompson > mthompson@seanet.com > > > > Hi, Mark, Please check: Hong Huixiao and Xin Xinquan, "ESSESA: An Expert System for Structure Elucidation from Spectra Analysis. 2. A Novel Algorithm of Perception of the Linear Independent Smallest Set of Smallest Rings", Analytica Chimica Acta, 1992, 262(2), 179-191. Huixiao From chemistry-request@server.ccl.net Tue Jun 15 20:25:50 1999 Received: from email.guomai.sh.cn (e3000.guomai.sh.cn [202.96.206.71]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA04150 for ; Tue, 15 Jun 1999 20:25:49 -0400 Received: from guomai.sh.cn ([210.74.253.86]) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.01.13.19.49.p4) with ESMTP id <0FDE006EI8QVSC@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Wed, 16 Jun 1999 08:16:52 +0800 (CST) Date: Wed, 16 Jun 1999 08:15:33 +0800 From: Yubo Fan Subject: How to scale the Entropy and Enthalpy? To: CHEMISTRY@ccl.net Message-id: <3766ECA5.DA187A7A@guomai.sh.cn> Organization: Fudan University 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 CCLers, I have done some freqency calculations recently and didn't add the scale data in these input files. Now I should scale the thermal analysis datas manually. How should I correct the entropies, enthalpies and free energies? Thank you very much. I am looking forward to receiving your reply. With best regards Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From chemistry-request@server.ccl.net Tue Jun 15 23:49:33 1999 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA05779 for ; Tue, 15 Jun 1999 23:49:30 -0400 Received: from voxopm-e.csc.fi (voxopm-e.csc.fi [128.214.46.23]) by pobox.csc.fi (8.9.0.Beta5/8.9.0.Beta5/CSC/Rtrs-1.22) with ESMTP id GAA08385 for ; Wed, 16 Jun 1999 06:41:41 +0300 (EET DST) Date: Wed, 16 Jun 1999 06:41:40 +0300 From: Maija Lahtela X-Sender: mlahtela@voxopm.minedu.fi To: chemistry@ccl.net Subject: Cartesian force constants in G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, We would appreciate your help in our problem dealing with Cartesian force constants in G98. We noticed that for small molecules options (#P PM3 Opt Freq )will print frequencies and force constants but for large molecules it doesn't print either frequencise nor force constants. For large molecules we have used the following options (#P PM3 Opt Freq Iop(7/29=1,7/33=1)). The problem is that by using Iop(7/29=1,7/33=1) the force constants are different than if is not used. Does anyone know why Freq-option doesn't print the IR-spektrum and force constants for large molecules ? THANKS IN ADVANCE! Sincerely Yours, Maija Lahtela-Kakkonen *************************************** Maija Lahtela-Kakkonen Researcher CSC-Center for Scientific Computing Tekniikantie 15 a D P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 FAX 358-9-4572302 E-MAIL mlahtela@csc.fi ***************************************