From toukie@zui.unizh.ch Fri Jul 5 03:58:27 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.5/950822.1) id DAA16699; Fri, 5 Jul 1996 03:07:46 -0400 (EDT) Received: from rzurs3.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA05330; Fri, 5 Jul 96 09:07:22 +0200 Received: by rzurs3.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA59600; Fri, 5 Jul 1996 09:07:18 +0200 From: toukie@zui.unizh.ch (Hr Dr. S. Shapiro) Message-Id: <9607050707.AA59600@rzurs3.unizh.ch> Subject: More re MOPAC IR To: chemistry@www.ccl.net Date: Fri, 5 Jul 1996 09:07:18 +0200 (MEST) Cc: chminf-l@iubvm.ucs.indiana.edu X-Mailer: ELM [version 2.4 PL24 PGP2] Content-Type: text Dear Colleagues; A few days ago I posted a query about how to implement MOPAC for the gene- ration of IR spectra. I thank the handful of people who took the time and ef- fort to respond. In a nutshell, one simply has to add the keyword FORCE, and a vibrational analysis will be added to the MOPAC output. (n.b.: In my imple- mentation of MOPAC 6.0, at least, the keywords FORCE and EF seem to be incompat- ible. Does anyone know why that might be?) One responder mentioned a very nice programme by Dr. J. Gosper of Brunel University (U. K.) which visualises the output structure from a MOPAC .out file and which can animate one vibration- al frequency at a time. Unfortunately, I do not believe that there yet exists a programme that will regenerate an IR spectrum as such from the output of a MOPAC "FORCE" calculation. (If I am wrong, kidly correct me.) As a result of the responses received, I was able to undertake an intelli- gent search through the local science libraries, and found a particularly use- ful article: SEEGER, D. M., KORZENIEWSKI, C., and KOWALCHYK, W., Evaluation of vibrational force fields derived by using semiempirical and ab initio methods. J. Phys. Chem. 95: 6871-6879. which lists experimental, semiempirical, and ab initio force constants and fre- quencies for a variety of molecules, as well as recommended sacling factors for different types of vibrations calculated using the MNDO, AM1, and PM3 parametri- sations. One of the responders mentioned that a Dr. Radom (Leo Radom?) has pub- lished, or has in press, an article further detailing vibrational frequency scaling factors for MOPAC- and ab initio-calculated molecular vibrational fre- quencies. However, I have been unavble to locate such an article. Does anyone out there know about this paper? If so, kindly post details. I now wish to follow up my original query about MOPAC and IR with these two questions: (i) The article cited above by Seeger et al. calculated MNDO, AM1, and PM3 scaling factors for hydroxyl O -- H stretches based only upon water. I am par- ticularly interested in a scaling factor for hydroxyl O -- H stretches in phenol and phenolic-type molecules, both simple (cresols, xylenols, methoxyphenols) and more complex (terpenoids, oestrogens, &c.). Has anyone seen an article in which a scaling factor for phenolic O -- H stretches is provided? (ii) In connection with the above, I am seeking values for phenolic O -- H stretching frequencies with reference to particular orientations of the phenolic hydroxy moieties vis-a'-vis the rest of the molecule. For example, in an old paper by Simonyi et al [Tetrah. Lett. (19): 1631-1632 (1975), the authors sug- gest that for 2,6-di-isopropylphenol the O -- H peak at 3641 cm-1 corresponds to the structure in which the hydroxy moiety is captured between the two methyls of the isopropyl unit, whereas the O -- H stretch at 3619 cm-1 is due to "a" conformation in which the hydroxy moiety is _not_ captured between a pair of isopropyl methyl units. Can anyone provide me with additional, especially more recent, references providing experimental phenolic O -- H stretch frequencies as a function of phenolic conformation? Thanks in advance to all responders. With kindest regards, (Dr.) S. Shapiro Inst. f. orale Mikrobiol. u. allg. Immunol. Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH Plattenstr. 11 Postfach CH-8028 ZH 7 Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From pyspag@bath.ac.uk Fri Jul 5 05:58:28 1996 Received: from goggins.bath.ac.uk for pyspag@bath.ac.uk by www.ccl.net (8.7.5/950822.1) id FAA17188; Fri, 5 Jul 1996 05:35:42 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Fri, 5 Jul 1996 10:35:13 +0100 Date: Fri, 5 Jul 1996 10:35:08 +0100 (BST) From: P A Gravil To: CHEMISTRY@www.ccl.net Subject: post-doc position available at Institut Francais du Petrole Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sir, Could you please send me details of the above post, which was recently advertised on the internet: I had problems loading the file, the end being corrupted. Thank you Yours sincerely Pete Gravil ------------------------------------------------------------ Dr. Peter Gravil School of Physics, Tel: +44 (0)1225 826826 Ext: 5237 University of Bath, Fax: +44 (0)1225 826110 Bath BA2 7AY, UK E-Mail: pyspag@bath.ac.uk ------------------------------------------------------------ From laaksone@csc.fi Fri Jul 5 06:52:28 1996 Received: from voxopm.minedu.fi for laaksone@csc.fi by www.ccl.net (8.7.5/950822.1) id FAA17161; Fri, 5 Jul 1996 05:27:03 -0400 (EDT) Received: (from laaksone@localhost) by voxopm.minedu.fi (8.7.5/8.6.11+CSC-2.0) id MAA01709; Fri, 5 Jul 1996 12:26:55 +0300 (EET DST) Content-Transfer-Encoding: 8bit Date: Fri, 5 Jul 1996 12:26:55 +0300 (EET DST) From: Leif Laaksonen X-Sender: laaksone@voxopm.minedu.fi To: chemistry@www.ccl.net Subject: Version 0.2 (alpha) of RTAM is now on line Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Computational Chemists, The DATABASE RTAM, Version 0.2 alpha (July 05, 1996). (C) Pekka Pyykko Pyykko, Department of Chemistry, University of Helsinki (E-mail: Pekka.Pyykko@helsinki.fi) is now available for search at: URL http://www.csc.fi/lul/rtam/ The database contains the bibliography part of the two books "Relativistic Theory of Atoms and Molecules I-II" (Springer, Berlin, 1986 and 1993), (LNCh 41 and 60) as well as additional references, mainly from 1993-6. The contents of the references are analyzed in the books. Yours, Leif Laaksonen Pekka Pyykko ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 0 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi ---------URL: http://laaksonen.csc.fi/leif.laaksonen.html---------- From chpajt@bath.ac.uk Fri Jul 5 07:59:13 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.5/950822.1) id HAA17602; Fri, 5 Jul 1996 07:18:34 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Fri, 5 Jul 1996 12:17:39 +0100 Date: Fri, 5 Jul 1996 12:17:32 +0100 (BST) From: A J Turner To: "Hr Dr. S. Shapiro" cc: chemistry@www.ccl.net, chminf-l@iubvm.ucs.indiana.edu Subject: Re: CCL:M:More re MOPAC IR In-Reply-To: <9607050707.AA59600@rzurs3.unizh.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! FORCE and EF are incompatable as FORCE auto uses BFGS to optimise if the gradients are too large. If you wish to use EF, optimise first, then take the output and FORCE that. Cheers Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From chd00@cc.keele.ac.uk Fri Jul 5 08:58:42 1996 Received: from gabriel.keele.ac.uk for chd00@cc.keele.ac.uk by www.ccl.net (8.7.5/950822.1) id IAA17923; Fri, 5 Jul 1996 08:38:40 -0400 (EDT) Received: from potter.cc.keele.ac.uk by gabriel.keele.ac.uk with SMTP (PP); Fri, 5 Jul 1996 13:38:39 +0100 From: "Ratty" Message-Id: <3669.199607051238@potter.cc.keele.ac.uk> Subject: add to MOPAC IR request... To: chemistry@www.ccl.net (chemmail) Date: Fri, 5 Jul 1996 13:38:34 +0100 (BST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Can someone give details of how to convert MOPAC vibrational analysis into RAMAN spectra too! Cheers Ratty chd00@potter.cc.keele.ac.uk From tamasgunda@tigris.klte.hu Fri Jul 5 09:07:35 1996 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.7.5/950822.1) id IAA17910; Fri, 5 Jul 1996 08:32:26 -0400 (EDT) Message-Id: <199607051232.IAA17910@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Fri, 05 Jul 1996 13:30:02 EDT Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Fri, 5 Jul 1996 13:15:33 +1 Subject: pK of thiols Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Dear Netters, I need the pK values of different aliphatic and (hetero)aromatic thiols, R-SH, to compare experimental and computed values. The data I found so far are quite sporadic. Could anybody suggest me a good source of these data? Best wishes Tamas E. Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From owner-chemistry@ccl.net Fri Jul 5 09:58:32 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id JAA18263; Fri, 5 Jul 1996 09:28:01 -0400 (EDT) Received: from valdivia.uca.uach.cl for raperez@valdivia.uca.uach.cl by bedrock.ccl.net (8.7.5/950822.1) id JAA01057; Fri, 5 Jul 1996 09:27:56 -0400 (EDT) Received: by valdivia.uca.uach.cl (AIX 3.2/UCB 5.64/4.03) id AA13086; Fri, 5 Jul 1996 09:24:47 -0400 Date: Fri, 5 Jul 1996 09:24:46 -0400 (EDT) From: "Dr. Ramiro Arratia Perez" Subject: Re: CCL:G:Software to view the orbitals from G94 To: Raja Amruthavalli Cc: chemistry@ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For the SGI there is a very good software called EXPLORER, you can view any grid of points and even you can plot 3D orbitals. Good luck, Ramiro Arratia Perez Instituto de Quimica Universidad Austral de Chile Valdivia Chile FAX (56)63-221599 e-mail: raperez@valdivia.uca.uach.cl From chd00@cc.keele.ac.uk Fri Jul 5 10:58:32 1996 Received: from gabriel.keele.ac.uk for chd00@cc.keele.ac.uk by www.ccl.net (8.7.5/950822.1) id KAA18566; Fri, 5 Jul 1996 10:29:45 -0400 (EDT) Received: from potter.cc.keele.ac.uk by gabriel.keele.ac.uk with SMTP (PP); Fri, 5 Jul 1996 15:29:38 +0100 From: "Ratty" Message-Id: <18108.199607051429@potter.cc.keele.ac.uk> Subject: add to MOPAC IR request (II) To: chemistry@www.ccl.net (chemmail) Date: Fri, 5 Jul 1996 15:29:34 +0100 (BST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Oh I forgot something rather important.... I need to model resonance raman spectra! (i.e. lots of nasty selection rules...) Ratty From tp@elptrs7.rug.ac.be Fri Jul 5 11:58:34 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.7.5/950822.1) id LAA18921; Fri, 5 Jul 1996 11:32:33 -0400 (EDT) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA22084; Fri, 5 Jul 1996 17:33:57 +0200 Date: Fri, 5 Jul 1996 17:33:57 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List Subject: Heat of formation calculation using MOPAC. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I have a question on the parameters in MOPAC. I'm tring to calculate the heat of formation for more or less 100 different gas-phase carbenium ions. Which parameter would be suitable for this calculation? PM3? AM1? I tried to compare the results obtained from MOPAC with a few experimental data available in the literature, and found that AM1 is much closer to those experimental data than the case of PM3 when the molecule contains the cabon atoms up to 5. According to the manual of MOAPC, however, PM3 is more improved parameter than AM1! My question is that the AM1 would also produce better result if the molecule becomes larger (upto C8)? Any suggestion would be greatly appreciated. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= State University of Ghent Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From arthur@csb0.IPC.PKU.EDU.CN Fri Jul 5 21:58:35 1996 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.7.5/950822.1) id VAA21194; Fri, 5 Jul 1996 21:35:40 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA23584; Sat, 6 Jul 96 09:33:59 -0700 Date: Sat, 6 Jul 1996 09:33:57 -0700 (PDT) From: Arthur Wang To: CCL mailing list Subject: Where to submit the paper? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Maybe you can answer this simple question in a nanosecond: Our lab has developed a new empirical method to calculate logP. For it is a relatively specific theme, some editors have suggested it should be submitted to some QSAR journals. So I would like to listen to your opinion: Which QSAR journal will be proper to submit our paper? Any answer will be great! Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2751490 Fax: 86-10-2751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/