From gadre@unipune.ernet.in Thu Nov 23 05:22:01 1995 Received: from sangam.ncst.ernet.in for gadre@unipune.ernet.in by www.ccl.net (8.6.10/950822.1) id FAA00781; Thu, 23 Nov 1995 05:07:01 -0500 Received: from unipune.UUCP (uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id PAA24396 for CHEMISTRY@www.ccl.net; Thu, 23 Nov 1995 15:37:27 +0530 Received: from unipune.UUCP by iucaa (4.1/SMI-4.1) id AA27720; Thu, 23 Nov 95 14:26:41+050 Received: by unipune.unipune.ernet.in (5.0/SMI-SVR4) id AA03600; Thu, 23 Nov 1995 13:46:49 +0500 Date: Thu, 23 Nov 1995 13:46:49 +0500 From: gadre@unipune.ernet.in (Faculty) Message-Id: <9511231846.AA03600@unipune.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Addresses for chemistry networks Cc: gadre@unipune.ernet.in Content-Length: 118 Dear Sirs: I will appreciate receiving addresses (internet) of Chemistry-related networks. Thanks!.....Shridhar Gadre From D.J.Wild@sheffield.ac.uk Thu Nov 23 05:37:02 1995 Received: from pp2.shef.ac.uk for D.J.Wild@sheffield.ac.uk by www.ccl.net (8.6.10/950822.1) id FAA01041; Thu, 23 Nov 1995 05:25:22 -0500 Received: from ramsley.shef.ac.uk by pp2.shef.ac.uk with local SMTP (PP); Thu, 23 Nov 1995 10:21:46 +0000 Received: from RAMSLEY/MAILQUEUE by ramsley.shef.ac.uk (Mercury 1.21); 23 Nov 95 10:21:46 +0000 Received: from MAILQUEUE by RAMSLEY (Mercury 1.21); 23 Nov 95 10:21:19 +0000 From: David Wild To: chemistry@www.ccl.net Date: Thu, 23 Nov 1995 10:21:13 +0000 Subject: Gaussians for electron density curves Reply-to: D.J.Wild@sheffield.ac.uk Priority: normal X-mailer: Pegasus Mail for Windows (v2.10) Message-ID: <1613E1C2730@ramsley.shef.ac.uk> Hi All As part of the work I'm doing, I need Gaussian expressions to fit to the electron density curves (i.e. plot of electron density against distance from the atom) for all of the common organic atom types. I have expressions for C, N, S, O and H that were apparently taken from the STO-3G set of the Gaus88 module of SYBYL, but unfortunately we don't have that module in our SYBYL here. If anyone has access to the STO-3G basis set, and would be willing to let me know the Gaussians for other common organic atoms (Cl, Br, Fl, I, P are the ones that spring to mind), I would be most grateful. Many thanks David Wild ------------------------------------------------- Dr David Wild, Department of Information Studies, University of Sheffield, Sheffield S10 2TN, U.K. Tel +44-(0)114 282 5093, Fax +44-(0)114 278 0300 Email D.J.Wild@sheffield.ac.uk http://www.shef.ac.uk/uni/academic/I-M/is/rstaff/ davewild.html From nervi@chpc06.ch.unito.it Thu Nov 23 09:22:05 1995 Received: from chpc06.ch.unito.it for nervi@chpc06.ch.unito.it by www.ccl.net (8.6.10/950822.1) id JAA03252; Thu, 23 Nov 1995 09:00:29 -0500 Received: (from nervi@localhost) by chpc06.ch.unito.it (8.6.9/8.6.9) id OAA03281; Thu, 23 Nov 1995 14:52:05 +0100 Date: Thu, 23 Nov 1995 14:52:02 +0100 From: Carlo Nervi Subject: Re: CCL:Addresses for chemistry networks To: Faculty cc: CHEMISTRY@www.ccl.net In-Reply-To: <9511231846.AA03600@unipune.unipune.ernet.in> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Dear Sirs: I will appreciate receiving addresses (internet) > of Chemistry-related networks. Thanks!.....Shridhar Gadre > I suppose you mean www general informations. Try the well-known http://www.chem.ucla.edu/chempointers.html or our pages (see below). Carlo Nervi ---------------------------------------------------------------------------- Dr. Carlo Nervi Dipartimento di Chimica Inorganica, Chimica Fisica e Chimica dei Materiali, via P. Giuria 7, 10125 Torino, ITALY phone: (Italy)-11-6707508 | e-mail: nervi@chpc06.ch.unito.it fax: (Italy)-11-6707855 | nervi@silver.ch.unito.it http://chpc06.ch.unito.it/ ---------------------------------------------------------------------------- From toukie@zui.unizh.ch Thu Nov 23 10:52:06 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id KAA04560; Thu, 23 Nov 1995 10:46:47 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA04687; Thu, 23 Nov 95 16:46:39 +0100 X-Nupop-Charset: Swiss Date: Thu, 23 Nov 1995 17:47:08 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <64028.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Diameter of a globular peptide Dear Colleagues; I was recently asked what would be the approximate theoretical diameters of globular peptides of molecuar weight 3,000 and 10,000. If anyone knows how to calculate this, I would be grateful if you would share with me the method of calculation. Kindest regards, S. Shapiro ZH, CH toukie@zui.unizh.ch From toukie@zui.unizh.ch Thu Nov 23 11:00:36 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id KAA04563; Thu, 23 Nov 1995 10:46:59 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA04674; Thu, 23 Nov 95 16:46:32 +0100 X-Nupop-Charset: Swiss Date: Thu, 23 Nov 1995 17:47:00 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <64020.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Two questions Dear Colleagues; I have two questions which I hope someone out in cyberspace will be able to answer, either individually or together: (i) Does anyone have information on the structure in solution of micelles of long-chain n-alkylphenols or alkoxyphenols, e.g. n-p- (or m- or o-) octylphenol, n-p- (or m- or o-) heptyl- phenol, n-p- (or m- or o-) octyloxyphenol, or n-p- (or m- or o-) heptyloxyphenol? Does anyone know of published values of solubilities or especially critical micelle concentrations of such compounds? (ii) Does anyone have any information on experimental (preferred) or theoretical (OK) values for the dielectric constant in the interior of lipid bilayers, artificial membranes, or (preferred) biological membranes? Thanks in advance to all responders. Regards, S. Shapiro ZH, CH toukie@zui.unizh.ch From kdr3@leicester.ac.uk Thu Nov 23 11:05:55 1995 Received: from venus.le.ac.uk for kdr3@leicester.ac.uk by www.ccl.net (8.6.10/950822.1) id KAA04487; Thu, 23 Nov 1995 10:38:21 -0500 Received: from hawk.le.ac.uk by venus.le.ac.uk with SMTP (PP); Thu, 23 Nov 1995 15:34:23 +0000 From: "Dr K.D. Roth" Message-Id: <4928.199511231528@hawk.le.ac.uk> Subject: Summary PSI88 & transition metals To: chemistry@www.ccl.net (ccl) Date: Thu, 23 Nov 1995 15:28:46 +0000 (GMT) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 4456 Hi fellow CCL'ers about two weeks ago I posted a question about plotting MO's from Gaussian cal- culations on transtion metal complexes using PSI88 or a similar program. Here is now the promised summary of the responses I got, I'm sorry for the delay which is due to two unforeseen absences. Anyway, here is what I got, special thanks to Tom Pollard, his modified PSI88 will probably be the best solution. I have not tried yet viewmol, I simply was not able to download the files from the servers, but I'll keep on trying. ******************************************************************************** From: > ------------------------------------------------------------------------- > W. Thomas Pollard Department of Chemistry > pollard@chem.columbia.edu Columbia University > ------------------------------------------------------------------------- > > I've actually done this extension to the rest of the periodic table. > Our version has also been modified to accept arbitrary Gaussian basis > sets, given an explicit list of the Gaussian primitives for each basis > function of each atom of the molecule. This sounds excessive, but we > do PSGVB calculations using ECP bases and with different basis sets for > different atoms (sometimes). It's been a while since I looked at it, > but it's likely that the extension to transition metals only works for > the explicitly described Gaussian basis sets. > > You're welcome to the code, if it sounds like what you want. From: > -------------------------- > Dr. Joerg-Ruediger Hill > Biosym/MSI > 9685 Scranton Road > San Diego, CA 92121-2777 > USA > > Phone (619) 546-5508 > Fax (619) 458-0136 > E-mail jxh@biosym.com > Paris, 1838 > -------------------------- > > Ich kann zwar nicht mit einer Erweiterung von PSI88 dienen, aber ich > habe einmal > ein Programm geschrieben, das Orbitale direkt von Gaussian-Outputs berechnen > und zeichnen kann (allerdings Gaussian92). Dieses Programm (Viewmol) kann > per anonymous ftp unter den folgenden Adressen bezogen werden: > ftp://www.ccl.net/pub/chemistry/software/SOURCES/C/viewmol > ftp://ftp.ask.uni-karlsruhe.de/pub/education/chemistry/viewmol.tar.gz. > Es laueft auf SGI- and IBM-Workstations und ist fuer akademische Nutzer frei. > > Joerg-Ruediger Hill From: > > | Oliver Hill > | Department of Chemistry > | University of Cape Town > | Rondebosch, 7700 > | SOUTH AFRICA > | oliver@psipsy.uct.ac.za (internet) > | > | Tel. +27-21-650-2527 > | Fax. +27-21-650-3788 > | > | http://www.cem.uct.ac.za/PeopleInChemDept/grad/oliver-hill.html > > Try Moplot2 which is in the CCL archives. > From: > William McCarthy > > Hello, we've also found psi88 to be limited (but with regard to basis sets). > However, I have found a way to display MOs and total density by utilizing > the "cube=orbitals" keyword is g92 (or g94), converting the format of > the output file with a small fortran program I wrote, then using the > rendering portion of programs of D. Lichtenberger's Moplot2 program. > I believe all of these programs are available via anonymous ftp (you > can use archie to find out where), and then all that you'd need is a > fortran compiler. I hope that this is what you're looking for. > Good Luck, Will McCarthy > ******************************************************************************** Apart from that I received two pointers to Spartan - sorry, I should have specified that I was looking for non-commercial software. This is especially to William McCarthy: I'd be grateful if you could send me your e-mail address and the name of your fortran program mentioned above - it would make searching for it much easier :-)... Again, thanks to everybody who answered Cheers and greetings from Leicester Dieter ******************************************************************************** + Dr. Klaus-Dieter Roth + I'm trying hard to prove Department of Chemistry + Murphy's law .... University of Leicester + Leicester LE1 7RH + ... but something always e-mail: kdr3@le.ac.uk + goes wrong ... + ******************************************************************************** From BAELL@mel.dah.csiro.au Thu Nov 23 21:52:14 1995 Received: from dahsun.mel.dah.csiro.au for BAELL@mel.dah.csiro.au by www.ccl.net (8.6.10/950822.1) id VAA11168; Thu, 23 Nov 1995 21:41:15 -0500 Received: from mhs.mel.dah.csiro.au (mhs.mel.dah.CSIRO.AU [192.94.209.40]) by dahsun.mel.dah.csiro.au (8.6.10/8.6.10) with SMTP id NAA23046 for <@dahsun.mel.dah.csiro.au:chemistry@www.ccl.net>; Fri, 24 Nov 1995 13:44:46 +1100 Message-Id: <199511240244.NAA23046@dahsun.mel.dah.csiro.au> From: BAELL@mel.dah.csiro.au (Jonathan Baell) To: chemistry@www.ccl.net (chemistry) Subject: solvent/binding/logP/R3N Date: Fri, 24 Nov 95 13:38 Dear All, A few questions: -------------------------------------------------------------------------- A: Does anyone have a pointer to a good general discussion of approaches to incorporate environmental effects on molecular conformation such as might be experienced in a protein binding site and in an aqueous solution): e.g the pros and cons of simple distance-dependent dielectric methods (incorporating a constant of 1 or maybe 4?/using MNDO ESP charges?); more complex continuum methods; explicit solvent molecule calculations; treatment of highly basic amino groups in a protein binding site. B: Related to A; Didesmethylchlorpromazine binds much more poorly to some sites than chlorpromazine. Its terminal amine (RCH2NH2) has been shown to be significantly more basic than that in chlorpromazine (RCH2NMe2) [which was unexpected as far as I'm concerned], so desolvation problems may account for its weaker activity, or perhaps loss of favourable binding by the two methyl groups; but has there been discussion in the literature on the general principles of alkyl-NH2 versus alkyl-NMe2 receptor-ligand effects, two groups which are highly prevalent in biologically active molecules? C: I have seen a number of studies where a linear relationship has been reported between nematocidal activity of C. elegans and affinity at binding sites in C. elegans, suggesting an absence of a lipophilic effect on transport, which is surprising for a whole organism assay if membrane-transport is required to reach the active site, and one would usually expect this to be the case. The dataset in these cases has a reasonable spread of logP values. The nature of these studies is such that the nematode is subjected continuously to toxin over a long time (16h), rather than as a bolus-type dose. Can anyone point me to a good discussion of the relationship between time/dosage regimen and logP/activity, and why the nature of an assay such as the C. elegans one cited above might minimize lipophilicity as being an observable modulator of toxicity? D (and potentially paradoxical c.f. question C): For a certain group of compounds, we have the following QSAR for larvicidal activity for a particular species of parasitic nematode: pLD50 = 2.11xpi - 0.782xpi^2 + 4.79 95%CI 0.72 0.21 0.49 T value 6.95 -8.92 n=10, s=0.205, Table T-test 2.37 (95%) Y-mean=5.469, Y-variance = 0.833 Variance explained by regression=95% F-ratio= 70.6, r=0.976, F(2,7,0.01)=9.55 What concerns me is the slope of 2.11. What does this mean biologically? I thought the slope in such equations was at most around unity for hydrophobically sensitive systems. Could this value be explained by contributions of a substituent both to molecular lipophilicity (transport in vivo) and to binding to a localised hydrophobic pocket? The assay involves continuous exposure to active constituent in an agar environment over several days. -------------------------------------------------------------- Any input would be greatly appreciated on any of these questions (including an internet address for a good QSAR discussion group, if there is one) Jonathan Ball email: ball@mel.dah.csiro.au or baell@mel.dah.csiro.au From SHANKSRA@bunyip.ph.rmit.edu.au Thu Nov 23 22:22:15 1995 Received: from peladon.rmit.EDU.AU for SHANKSRA@bunyip.ph.rmit.edu.au by www.ccl.net (8.6.10/950822.1) id WAA11370; Thu, 23 Nov 1995 22:14:11 -0500 Received: from bunyip.ph.rmit.edu.au (bunyip.ph.rmit.EDU.AU [131.170.248.94]) by peladon.rmit.EDU.AU (8.7/8.6.9) with SMTP id OAA18788 for ; Fri, 24 Nov 1995 14:14:04 +1100 (EST) Received: from BUNYIP/SMTPQUEUE by bunyip.ph.rmit.edu.au (Mercury 1.13); Fri, 24 Nov 95 14:14:04 +1100 Received: from SMTPQUEUE by BUNYIP (Mercury 1.13); Fri, 24 Nov 95 14:13:55 +1100 From: "Assoc. Prof. Robert A. Shanks" Organization: RMIT Applied Physics To: CHEMISTRY@www.ccl.net Date: Fri, 24 Nov 1995 2:13:51 EST-10 Subject: Chemistry WWW Addresses Reply-to: ShanksRA@rmit.edu.au Priority: normal X-mailer: Pegasus Mail/Mac (v2.1.2) Message-ID: <372F0DA02E3@bunyip.ph.rmit.edu.au> The following are two new WWW addresses for information about RMIT University, Applied Chemistry Dept and Rheology and Materials Processing Centre. http://www.rmit.edu.au/departments/cm/ http://www.rmit.edu.au/departments/ch/rmpc/ Robert Shanks __________________________________ Assoc. Prof. Robert A. Shanks Associate Professor of Polymer Science Department of Applied Chemistry Royal Melbourne Institute of Technology Box 2476V GPO Melbourne Victoria 3001 Australia Telephone and Fax +61 3 6602122 Mobile Telephone +61 041 935 8001 __________________________________ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + + + 37th. IUPAC International Symposium on Macromolecules + + Gold Coast Australia, 13-17th July 1998 + + + + ,-_|\ macro98@chem.chemistry.uq.edu.au + + / \MACRO98 http://www.uq.edu.au/~cmawhitt/macro98.html + + \_,-._/ + + v + + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From arthur@csb0.IPC.PKU.EDU.CN Thu Nov 23 22:28:07 1995 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id WAA11319; Thu, 23 Nov 1995 22:05:00 -0500 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA12829; Fri, 24 Nov 95 11:02:58 -0800 Date: Fri, 24 Nov 1995 11:02:58 -0800 (PST) From: Arthur Wang To: CCL mailing list Subject: Convert 3D structure to 2D structure? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, dear CCLers, Are there any softwares whcih can convert 3D structures of small organic compounds from, say, MOL2 or PDB format to comfortable 2D topological structures? It is not a strange question. Maybe you will like to show a structure derived from molecular modeling software on a piece of paper. In this case, projection of the 3D structure does not work because it is not in the favor of organic chemists. You can draw it by yourself but when there are dozens of structures, it becomes a disturbing job. Any ideas? Thanks in advance. 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: 86-10-2501490 Fax: 86-10-2501725 _/ _/ WWW: http://www.ipc.pku.edu.cn/arthur/homepage.html _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From hiroshi@U.Arizona.EDU Thu Nov 23 23:22:16 1995 Received: from bonaire.ccit.arizona.edu for hiroshi@U.Arizona.EDU by www.ccl.net (8.6.10/950822.1) id XAA12111; Thu, 23 Nov 1995 23:20:06 -0500 Received: (from hiroshi@localhost) by bonaire.ccit.arizona.edu (8.6.12/8.6.12) id VAA31751; Thu, 23 Nov 1995 21:23:22 -0700 Date: Thu, 23 Nov 1995 21:23:22 -0700 (MST) From: Hiroshi Ogura X-Sender: hiroshi@bonaire.ccit.arizona.edu To: CompChem List Subject: Spartan: Fe parameters for semiempirical calculations? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to attempt semiempircal calculations (AM1 or PM1) of iron porphyrin complexes with Spartan. Unfortunately, our computer does not have the parameters for iron. Could anybody please tell me if the parameters are available somewhere? Thanks. -- Hiroshi Ogura | One man, he drinks up his whiskey, hiroshi@u.arizona.edu | Another, he drinks up his wine. Dept. Chem., Univ. Az. | And they'll drink till their eyes are red with hate Tucson, AZ 85721 | For those of a different kind. -- Richard Thompson From hiroshi@U.Arizona.EDU Thu Nov 23 23:30:34 1995 Received: from bonaire.ccit.arizona.edu for hiroshi@U.Arizona.EDU by www.ccl.net (8.6.10/950822.1) id XAA11910; Thu, 23 Nov 1995 23:11:52 -0500 Received: (from hiroshi@localhost) by bonaire.ccit.arizona.edu (8.6.12/8.6.12) id VAA34789; Thu, 23 Nov 1995 21:15:08 -0700 Date: Thu, 23 Nov 1995 21:15:08 -0700 (MST) From: Hiroshi Ogura X-Sender: hiroshi@bonaire.ccit.arizona.edu To: CompChem List Subject: Spartan: a multiplicity problem with a porphyrin Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am a relatively new user of Spartan. A while ago, I was attempting an ab-initio calculation for a diacid form of octamethyl tetraphenyl porphyrin (H2OMTPP), a nonplanar species. When the program asked for the multiplicity, I indicated that it was 1 -- the molecule is diamagnetic. Very soon after I submitted the calculation, the program sent me an error message: it said that singlet multiplicity was impossible with this molecule! I certainly do know that H2OMTPP is diamagnetic, just like any other nonmetallated porphyrin. Moreover, when I submitted an ab-initio calculation for the diacid form of the simplest porphyrin -- the one with hydrogens in all of the peripheral positions -- the program did not complain with my assignment of singlet multiplicity. How could the nonplanar distortion of H2OMTPP cause the program to think that the molecule could not be singlet? Thanks in advance. -- Hiroshi Ogura | One man, he drinks up his whiskey, hiroshi@u.arizona.edu | Another, he drinks up his wine. Dept. Chem., Univ. Az. | And they'll drink till their eyes are red with hate Tucson, AZ 85721 | For those of a different kind. -- Richard Thompson