From chemistry-request@server.ccl.net Thu Sep 14 02:02:13 2000 Received: from chem.ufl.edu (server.chem.ufl.edu [128.227.16.141]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA20073 for ; Thu, 14 Sep 2000 02:02:12 -0400 Received: from chem.ufl.edu (chem.ufl.edu [128.227.32.141]) by chem.ufl.edu (8.9.1/8.9.1/map) with ESMTP id CAA12640 for ; Thu, 14 Sep 2000 02:01:50 -0400 (EDT) Date: Thu, 14 Sep 2000 02:01:50 -0400 (EDT) From: "Xiang(Simon) Wang" To: CHEMISTRY@ccl.net Subject: Summary for I/O in Charmm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: Here is the summary for the answers to my original question of last week. Sorry for my late summary. I worked it out by following Rick Venable's suggestion: editing the existing RTF files. It works well with the academic version of Charmm if the suitable RTF files are available. I don't have QUANTA at hand, so I didn't try the the parameter chooser. Thanks a lot for all the answers. X. WANG --------------------------------------------------------------------- Original Question: Can someone help me on how to read small molecule structure in Charmm? For example, phosphoribosyldiphosphate (PRPP), which can not be found in top_all22_model.inp file. I could get the PSF file from InsightII. But when running, Charmm gave the warning of lacking of parameters. Can someone help me out of it? ---------------------------------------------------- Jerome Baudry, Ph.D. The best approach would be to go for ab initio parametrization for your molecule. However, if you are using C25 or higher, there should be a 'automated parameters calculator' in CHARMM that can estimate missing parameters from the atom types. Now if insightII produces atom types that are not in CHARMM's parameter file, CHARMM will not be able to estimate the missing parameters. I suggest that you compare all the atom types assigned by Insight to the atom types defined in CHARMM's parameter file. If you find differences, you might want to change the atom type in the psf to the corrresponding type in the parameter file. ---------------------------------------------------- Rick Venable If you want results of reasonable quality, you should create the new molecule yourself, by editing a copy of an existing RTF file (one for nucleic acids might be best) to create the PRPP molecule as a RESIdue description using existing RESIdues as models to pick the correct atom parameter types. ---------------------------------------------------- Dr. Don Gregory Really, there are two separate issues here; (a) using InsightII to create CHARMm input files, and (b) what to do when a chosen force-field is missing parameters. The easy one first: Indeed, InsightII can write CHARMm PSF and RTF files. Whenever your research leads you to modify the (more or less) 'standard' molecule/residue types that are provided in the RTF files that come with InsightII, we heartily recommend you use the PSF creation capabilities of InsightII to make the 'whole-system' unique molecular topology description that CHARMm needs, i.e. the PSF file. That is what this capability is intended for. However, even given this, missing parameters are still a possibility since creating a topology is trivial comapred to developing a well optimized force-field that will cover all the esoteric molecular types you might encounter in your on-going research. MSI provides numerous force-fields, and are committed to extending our force-field coverage as we go forward. However if the force-field you are using (not specified in the original email) is missing parameters, we'd suggest CFF if that is not being used already. If CFF also is missing the parameters, then we're in the same boat as we've seen in dozens of emails here on the CCL, i.e. you can research the literature to see if someone has developed parameters *for that specific force-field* (if for another force-field, then you have to make the decision as to whether to accept the *approximation* that those parameters will be reasonably transferrable into the force-field you would like to use), or you can ask your collegues on CCL. --------------------------------------------------- Dr. Rebecca Rone If you have a copy of QUANTA that molecule should be no problem. Use CHEMNOTE and its RTF generator. If it finds missing parameters, which it shouldn't, it will recommend parameters from the parameter chooser. Be certain first that all the atom types are properly assigned, i.e. mimic the similar atom types as found in the DNA generator with approprate changes. Then accept the parameters as suggested and write the PSF. Also use the DNA generator to create a standard PSF and cross check the parameters. From chemistry-request@server.ccl.net Wed Sep 13 18:55:15 2000 Received: from hotmail.com (f25.law3.hotmail.com [209.185.241.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA18098 for ; Wed, 13 Sep 2000 18:55:14 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 13 Sep 2000 15:53:13 -0700 Received: from 128.101.39.55 by lw3fd.law3.hotmail.msn.com with HTTP; Wed, 13 Sep 2000 22:53:13 GMT X-Originating-IP: [128.101.39.55] From: "Y Z" To: CHEMISTRY@ccl.net Subject: Molecular structure needed Date: Wed, 13 Sep 2000 18:53:13 EDT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 13 Sep 2000 22:53:13.0585 (UTC) FILETIME=[65949610:01C01DD5] Hi, everyone: I need to find some experiemental molecular geometric structure results about some very simple molecules in aqueous solution. (1)H2O (2)CH3OH (3)CH3CN (4)CH3CO2- (anion) (5)NH3 I also hope to find the experimental value for the NaCl lattice energy. Could somebody can tell me some literatures? I need the newest original results. Thank you in advance. _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. Share information about yourself, create your own public profile at http://profiles.msn.com. From chemistry-request@server.ccl.net Thu Sep 14 03:09:21 2000 Received: from mailhub.unibe.ch (mailhub.unibe.ch [130.92.254.109]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA20405 for ; Thu, 14 Sep 2000 03:09:20 -0400 Received: from CONVERSION-DAEMON by mailhub.unibe.ch (PMDF V5.2-32 #42480) id <0G0V00G017PGX0@mailhub.unibe.ch> for CHEMISTRY@ccl.net; Thu, 14 Sep 2000 09:05:45 +0200 (MET DST) Received: from ubecx01 (ubecx01.unibe.ch [130.92.6.40]) by mailhub.unibe.ch (PMDF V5.2-32 #42480) with ESMTP id <0G0V00CKC7PFVI@mailhub.unibe.ch> for CHEMISTRY@ccl.net; Thu, 14 Sep 2000 09:05:40 +0200 (MET DST) Received: from issi.unibe.ch (trace.unibe.ch [130.92.76.65]) by ubecx01.unibe.ch (PMDF V5.2-32 #42481) with ESMTP id <0G0V00BCZ7V2YW@ubecx01.unibe.ch> for CHEMISTRY@ccl.net; Thu, 14 Sep 2000 09:09:02 +0200 (MET DST) Date: Thu, 14 Sep 2000 09:29:30 +0200 From: Stephan Graf Subject: CCL:dipole moment of charged molecule Sender: michael.graf-buhlmann@theol.unibe.ch To: CCL Message-id: <39C07E5A.A024E6DC@issi.unibe.ch> MIME-version: 1.0 X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5 i686) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en References: Hello, the dipole moment has contributions from two terms: mu = + Sum_a(Z_a * R_a) The first term is due to n electrons and the second term is the contribution of the N nuclei. - Sum_i(r_i) is the electronic dipole operator over all n electrons - Z_a and R_a are the nuclear charges and positions When the coordinate system is translated by r_0, one obtains the following equation: mu = + Sum_a(Z_a * (R_a-r_0)) mu = + + Sum_a(Z_a * R_a) - Sum_a(Z_a * r_0) mu = + Sum_a(Z_a * R_a) + - r_0 * Sum_a(Z_a) The first and second term are the same as in the equation without translation, and the third one is equal to n*r_0 and we get: mu = + Sum_a(Z_a * R_a) + r_0 *(n - Sum_a(Z_a)) In a neutral molecule the number of electrons is equal to the sum of the nuclear charges and the third term is zero. But this is not the case for charged ions. Regards, Stephan "Dr. Peter Burger" wrote: > > Dear CCLers, > > somehow I got stuck. I want to calculate and compare (DFT) the dipole > moments for a series of > > charged molecules (monocations). > > Is this possible? I noticed a severe problem, so far, > which I believe is in part due to the choice of reference point > (so far center of mass). > > Any pointer is highly appreciated. > > Peter > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Dr. Stephan Graf International Space Science Institute Hallerstrasse 6 Phone : ++41/31/631 32 54 CH-3012 Bern Fax : ++41/31/631 48 97 Switzerland email : stephan.graf@issi.unibe.ch From chemistry-request@server.ccl.net Thu Sep 14 04:12:43 2000 Received: from indyio.rz.uni-sb.de (indyio.rz.uni-sb.de [134.96.7.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA20929 for ; Thu, 14 Sep 2000 04:12:42 -0400 Received: from mars.rz.uni-sb.de (ns0.rz.uni-sb.de [134.96.7.5]) by indyio.rz.uni-sb.de (8.9.3/8.9.3) with ESMTP id KAA14243027; Thu, 14 Sep 2000 10:12:29 +0200 (CST) Received: from pb11rh08 (pb11rh05.pharma.uni-sb.de [134.96.192.149]) by mars.rz.uni-sb.de (8.8.8/8.8.4/8.8.2) with ESMTP id KAA00741; Thu, 14 Sep 2000 10:12:29 +0200 (CST) From: "Christoph Jacobs" To: "Trevor Kramer" , chemistry@ccl.net Date: Thu, 14 Sep 2000 10:19:52 +0200 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Reusing autogrid maps in autodock Reply-to: c.jacobs@rz.uni-sb.de Message-ID: <39C0A648.31328.713C20@localhost> X-Confirm-Reading-To: c.jacobs@rz.uni-sb.de X-pmrqc: 1 Priority: normal In-reply-to: <968711513_PM_BeOS.tkramer@hampshire.edu> X-mailer: Pegasus Mail for Win32 (v3.12c) Dear Trevor, for my opinion you can reuse your gridmaps without any problem. A grid map represents only the proberties of your macromolecule in respects of the probes used to creat it (elements of your ligand) and it shoud be the same for one atom type and independ of the ligand. Then your ligand is docked to this gridmaps. If your ligands consist of different elements only the gridmaps for the elements in your actual ligand are needed. Christoph Jacobs FR 12.1 Pharmazeutische und Medizinische Chemie Gebaeude 32 Universitaet des Saarlandes 66041 Saarbruecken From chemistry-request@server.ccl.net Thu Sep 14 04:37:55 2000 Received: from chemistry.leeds.ac.uk (chmsun1.leeds.ac.uk [129.11.136.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA21082 for ; Thu, 14 Sep 2000 04:37:50 -0400 Received: from chmibm275 (chmibm275.leeds.ac.uk [129.11.137.177]) by chemistry.leeds.ac.uk (8.9.0/8.9.0) with SMTP id JAA27608; Thu, 14 Sep 2000 09:37:39 +0100 (BST) Message-Id: <3.0.6.32.20000914093235.007e7610@chmsun1.leeds.ac.uk> X-Sender: wolfgang@chmsun1.leeds.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 14 Sep 2000 09:32:35 +0100 To: "Y Z" From: Wolfgang Roth Subject: Re: CCL:Molecular structure needed Cc: CHEMISTRY@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear "Y Z", given the simplicity of the molecules you are looking for, I clearly understand your need to remain anonymous. However it should be fairly easy to retrieve those information by either walking to your local library (chemistry/physics) or searching the internet using altavista. In my opinion, the retrieval of information is an important part of researchers education. Regards Wolfgang >I need to find some experiemental molecular geometric structure results >about some very simple molecules in aqueous solution. > >(1)H2O >(2)CH3OH >(3)CH3CN >(4)CH3CO2- (anion) >(5)NH3 > >I also hope to find the experimental value for the NaCl lattice energy. > >Could somebody can tell me some literatures? ==W=R==========================W=o=l=f=g=a=n=g==R=o=t=h== University of Leeds School of Chemistry Leeds LS2 9JT UK ========== http://home.germany.net/100-500777/ ========== From chemistry-request@server.ccl.net Thu Sep 14 05:21:48 2000 Received: from dns.campus.mlsultan.ac.za ([196.26.161.245]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21274 for ; Thu, 14 Sep 2000 05:21:44 -0400 Received: from wpogate.mlsultan.ac.za (wpogate.campus.mlsultan.ac.za [196.26.161.11]) by dns.campus.mlsultan.ac.za (AIX4.2/UCB 8.7/8.7) with SMTP id LAA08102 for ; Thu, 14 Sep 2000 11:34:33 +0300 (USADT) Received: from MLSTGW-Message_Server by wpogate.mlsultan.ac.za with Novell_GroupWise; Thu, 14 Sep 2000 11:20:43 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5.3 Date: Thu, 14 Sep 2000 11:20:39 +0200 From: "Thishana Singh" To: , , " Subject: Conferences Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA21275 Hello CCLers I am not sure if this is the correct forum to ask this question. I would like to find out if there are any conferences (Computational Chemistry) being organised or scheduled for the period January 2001 to August 2001, in the UK and Europe. I will summary the responses. Thank you. Thishana Singh Department of Chemistry 41/43 Centennary Road Durban 4001 South Africa Tel : +27 31 3085521 Fax : +27 31 3085400 email : singht@wpo.mlsultan.ac.za From chemistry-request@server.ccl.net Thu Sep 14 05:21:49 2000 Received: from dns.campus.mlsultan.ac.za ([196.26.161.245]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21273; Thu, 14 Sep 2000 05:21:40 -0400 Received: from wpogate.mlsultan.ac.za (wpogate.campus.mlsultan.ac.za [196.26.161.11]) by dns.campus.mlsultan.ac.za (AIX4.2/UCB 8.7/8.7) with SMTP id LAA08096; Thu, 14 Sep 2000 11:34:26 +0300 (USADT) Received: from MLSTGW-Message_Server by wpogate.mlsultan.ac.za with Novell_GroupWise; Thu, 14 Sep 2000 11:20:43 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5.3 Date: Thu, 14 Sep 2000 11:20:39 +0200 From: "Thishana Singh" To: , , " Subject: Conferences Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA21279 Hello CCLers I am not sure if this is the correct forum to ask this question. I would like to find out if there are any conferences (Computational Chemistry) being organised or scheduled for the period January 2001 to August 2001, in the UK and Europe. I will summary the responses. Thank you. Thishana Singh Department of Chemistry 41/43 Centennary Road Durban 4001 South Africa Tel : +27 31 3085521 Fax : +27 31 3085400 email : singht@wpo.mlsultan.ac.za From chemistry-request@server.ccl.net Thu Sep 14 13:02:35 2000 Received: from sdnt1.Acadia-SD (mail.acadia-pharm.com [209.77.18.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA24285 for ; Thu, 14 Sep 2000 13:02:34 -0400 Received: by sdnt1 with Internet Mail Service (5.5.2650.21) id ; Thu, 14 Sep 2000 10:02:18 -0700 Message-ID: <15189A4705A8D31189B700805F85410B413E90@sdnt1> From: Daniel Severance To: "'Jianxin Guo'" Cc: "'chemistry@ccl.net'" Subject: RE: alignment and QSAR? Date: Thu, 14 Sep 2000 10:02:18 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Hi Jianxin, Imagine that you had crystal structures of all of the molecules bound into an enzyme. Wouldn't you use that alignment for your studies instead of a simple template based one? I do drug discovery on projects involving GPCR systems. Thus I have no crystal structures (as I'm assuming you also are lacking). I have had a great deal of success using both pharmacophore tools and field analysis to be predictive. I have two different projects where the "correct" alignment of molecules was NOT the simple template based one. If one used the obvious template of the parts that were very similar, then the other parts of the molecule were difficult to explain. But, when using even the simplest concepts of conformational analysis and aligning against what interactions are likely with the receptor, the templates don't align in the obvious way, but what falls out of further analysis is that the rest of the molecule makes sense. In addition, one can predict that the space occupied by the template in one molecule, must be available for the second, and that has also been verified. Sorry I can't show you pictures of them, but eventually I'll publish it - both make nice stories. The short answer is that the pharmacophore alignment (done carefully) is the better one, IMHO. :-) Take care, Dan ____________________________________________________ Daniel L. Severance Ph.D. Computational Chemistry ACADIA Pharmaceuticals 3911 Sorrento Valley Boulevard San Diego CA 92121-1402 USA phone (858) 558 2871 fax (858) 558 2872 dseverance@acadia-pharm.com www.acadia-pharm.com -----Original Message----- From: Jianxin Guo [mailto:guojx@yahoo.com] Sent: Monday, September 11, 2000 5:50 PM To: chemistry@ccl.net Subject: CCL:alignment and QSAR? Hi, CCLers, Most of commercial software for 3D or 4D QSAR required for alignment of the molecules. Which is necessary for the field analysis (especially for CoMFA) and 3D descriptors. However, we know the tooplogy of the molecules structure determine the possibility of the alignment.so there must be some mothods to avoid the slow alignment. Are there any good papers for discussing this issue? Even for the alignment, the so-called pharmacophore or template should be used. The idea is similar, which is better? The pharmacophore asked information about the docking packet. so template is simpler as a starting point? Thanks, Jianxin __________________________________________________ Do You Yahoo!? Yahoo! Mail - Free email you can access from anywhere! http://mail.yahoo.com/ -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Sep 14 05:42:47 2000 Received: from mel.ruc.dk (mel.ruc.dk [130.225.220.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21422 for ; Thu, 14 Sep 2000 05:42:47 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id LAA10570 for ; Thu, 14 Sep 2000 11:42:38 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id LAA07468 for ; Thu, 14 Sep 2000 11:33:00 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 14 Sep 00 11:42:38 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 14 Sep 00 11:42:29 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: CHEMISTRY@ccl.net Date: Thu, 14 Sep 2000 11:42:05 +0100 Subject: CCL: Aromaticity, pi and sigma? Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: Dear CCL: I saw some time ago a paper with a theoretical analysis of the origin of "aromaticity" in benzene (and possibly other species), concluding that the so-called aromatic stability originated from the sigma-system rather than the pi-system. However, I cannot trace the original reference. Anybody knows it? Have additional work been published in this field? Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Sep 14 11:43:26 2000 Received: from hotmail.com (f209.law3.hotmail.com [209.185.241.209]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA23969 for ; Thu, 14 Sep 2000 11:43:25 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 14 Sep 2000 08:41:12 -0700 Received: from 128.101.39.67 by lw3fd.law3.hotmail.msn.com with HTTP; Thu, 14 Sep 2000 15:41:12 GMT X-Originating-IP: [128.101.39.67] From: "Y Z" To: Wolfgang.Roth1@epost.de Cc: CHEMISTRY@ccl.net Subject: Re: CCL:Molecular structure needed Date: Thu, 14 Sep 2000 11:41:12 EDT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 14 Sep 2000 15:41:12.0930 (UTC) FILETIME=[36144420:01C01E62] Dear Sir: My question and your answer can be summary as: (1)A=> >I need to find some experimental molecular geometric structure results > >about some very simple molecules in aqueous solution. (2)B=>However it should be fairly easy to retrieve those information by either >walking to your local library (chemistry/physics) or searching the internet >using altavista. (3)A doesn't mean I haven't done B. It doesn't mean I don't have data. I just asked question. No more extension. No more assumption. (4)C=>In my opinion, the retrieval of information is an important part of >researchers education. It is. But what is the relation with my question and your "suggestion"? (5)A doesn't mean I have no ability to DO C. There have no logical relationship between A and C. ======================== Question:A Answer: B+C This this a correct pattern by scientific discussion and query? I wonder as a scientist. ======================== Sorry for my personal opinion. >From: Wolfgang Roth >To: "Y Z" >CC: CHEMISTRY@ccl.net >Subject: CCL:Molecular structure needed >Date: Thu, 14 Sep 2000 09:32:35 +0100 > >Dear "Y Z", > >given the simplicity of the molecules you are looking for, I clearly >understand your need to remain anonymous. > >However it should be fairly easy to retrieve those information by either >walking to your local library (chemistry/physics) or searching the internet >using altavista. > >In my opinion, the retrieval of information is an important part of >researchers education. > >Regards >Wolfgang > > >I need to find some experiemental molecular geometric structure results > >about some very simple molecules in aqueous solution. > > > >(1)H2O > >(2)CH3OH > >(3)CH3CN > >(4)CH3CO2- (anion) > >(5)NH3 > > > >I also hope to find the experimental value for the NaCl lattice energy. > > > >Could somebody can tell me some literatures? > > > >==W=R==========================W=o=l=f=g=a=n=g==R=o=t=h== > University of Leeds > School of Chemistry > Leeds LS2 9JT > UK >========== http://home.germany.net/100-500777/ ========== > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net >70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: >jkl@ccl.net > > > > > _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. Share information about yourself, create your own public profile at http://profiles.msn.com. From chemistry-request@server.ccl.net Thu Sep 14 15:31:44 2000 Received: from euch4e.chem.emory.edu (euch4e.chem.emory.edu [170.140.59.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA24975 for ; Thu, 14 Sep 2000 15:31:44 -0400 Received: (from dima@localhost) by euch4e.chem.emory.edu (AIX4.2/UCB 8.7/8.7) id PAA40998; Thu, 14 Sep 2000 15:31:38 -0400 (EDT) From: Dmitry Khoroshun Message-Id: <200009141931.PAA40998@euch4e.chem.emory.edu> Subject: Re: CCL:Molecular structure needed To: yz0@hotmail.com (Y Z) Date: Thu, 14 Sep 2000 15:31:36 -0400 (EDT) Cc: CHEMISTRY@ccl.net In-Reply-To: from "Y Z" at Sep 14, 2000 11:41:12 AM X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! Being a logical person, you may have taken a look at the rules of CCL (although being totally abstract, your question *does* appear on CCL): http://www.ccl.net/chemistry/aboutccl/rules/ Particularly, at the lines: Unacceptable Topics Topics which may not appear on this list include: personal attacks topics unrelated to computational chemistry ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ It doesn't look like your question is obviously related to computational chemistry. Does it to you? Sincerely, Dmitry Khoroshun dima@euch4e.chem.emory.edu According to Y Z: > > > Dear Sir: > > My question and your answer can be summary as: > > (1)A=> >I need to find some experimental molecular geometric structure > results > > >about some very simple molecules in aqueous solution. > > (2)B=>However it should be fairly easy to retrieve those information by > either > >walking to your local library (chemistry/physics) or searching the > internet > >using altavista. > > (3)A doesn't mean I haven't done B. It doesn't mean I don't have data. I > just asked > question. No more extension. No more assumption. > > (4)C=>In my opinion, the retrieval of information is an important part of > >researchers education. > > It is. But what is the relation with my question and your "suggestion"? > > (5)A doesn't mean I have no ability to DO C. > > There have no logical relationship between A and C. > > ======================== > > Question:A > > Answer: B+C > > > This this a correct pattern by scientific discussion and query? I wonder as > a scientist. > > ======================== > > Sorry for my personal opinion. > > > > > >From: Wolfgang Roth > >To: "Y Z" > >CC: CHEMISTRY@ccl.net > >Subject: CCL:Molecular structure needed > >Date: Thu, 14 Sep 2000 09:32:35 +0100 > > > >Dear "Y Z", > > > >given the simplicity of the molecules you are looking for, I clearly > >understand your need to remain anonymous. > > > >However it should be fairly easy to retrieve those information by either > >walking to your local library (chemistry/physics) or searching the internet > >using altavista. > > > >In my opinion, the retrieval of information is an important part of > >researchers education. > > > >Regards > >Wolfgang > > > > >I need to find some experiemental molecular geometric structure results > > >about some very simple molecules in aqueous solution. > > > > > >(1)H2O > > >(2)CH3OH > > >(3)CH3CN > > >(4)CH3CO2- (anion) > > >(5)NH3 > > > > > >I also hope to find the experimental value for the NaCl lattice energy. > > > > > >Could somebody can tell me some literatures? > > > > > > > >==W=R==========================W=o=l=f=g=a=n=g==R=o=t=h== > > University of Leeds > > School of Chemistry > > Leeds LS2 9JT > > UK > >========== http://home.germany.net/100-500777/ ========== > > > >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > >Admins > >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > >70 > >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > >jkl@ccl.net > > > > > > > > > > > > _________________________________________________________________________ > Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. > > Share information about yourself, create your own public profile at > http://profiles.msn.com. > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Sep 14 16:27:41 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA25293 for ; Thu, 14 Sep 2000 16:27:41 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id QAA29661; Thu, 14 Sep 2000 16:27:39 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 14 Sep 2000 16:27:19 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com (lvlxch01.unitedcatalysts.com [10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G0W003GT8OP6J@lvlmail.unitedcatalysts.com>; Thu, 14 Sep 2000 16:24:25 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Thu, 14 Sep 2000 16:26:06 -0400 Content-return: allowed Date: Thu, 14 Sep 2000 16:26:03 -0400 From: "Shobe, Dave" Subject: RE: Aromaticity, pi and sigma? To: "'Jens Spanget-Larsen'" , CHEMISTRY@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D63856C@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id QAA25294 This may or may not be the one you're looking for, but here goes: Sason S. Shaik; Philippe C. Hiberty When Does Electronic Delocalization Become a Driving Force of Molecular Shape and Stability? The "Aromatic" Sextet J.Amer.Chem.Soc. 1985, 107 : 11 3089-3095. The argument isn't really that the "aromaticity" is in the sigma system, but that the sigma system is what allows an aromatic ground state (instead of a transition state like that of the Cope rearrangement). Benzene is stable and a regular hexagon because it meets *two* criteria, a sigma system that favors equal bond lengths, and a pi system that doesn't penalize equality of bond lengths greatly. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Any opinions herein are not necessarily representative of Süd-Chemie. -----Original Message----- From: Jens Spanget-Larsen [mailto:jsl@virgil.ruc.dk] Sent: Thursday, September 14, 2000 6:42 AM To: CHEMISTRY@ccl.net Subject: CCL:Aromaticity, pi and sigma? Dear CCL: I saw some time ago a paper with a theoretical analysis of the origin of "aromaticity" in benzene (and possibly other species), concluding that the so-called aromatic stability originated from the sigma-system rather than the pi-system. However, I cannot trace the original reference. Anybody knows it? Have additional work been published in this field? Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Sep 14 17:31:23 2000 Received: from usintout02.net.bms.com (usintout02.bms.com [165.89.129.232]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA25841 for ; Thu, 14 Sep 2000 17:31:22 -0400 Received: from nsusmsg03.net.bms.com ([127.0.0.1]) by mochilla.bms.com (PMDF V5.2-32 #38482) with ESMTP id <0G0W00D81BRP3C@mochilla.bms.com> for chemistry@ccl.net; Thu, 14 Sep 2000 21:31:01 +0000 (GMT) Received: from bms.com ([140.176.4.180]) by nsusmsg03.net.bms.com (Netscape Messaging Server 4.15) with ESMTP id G0WBRP00.10K; Thu, 14 Sep 2000 21:31:01 +0000 Date: Thu, 14 Sep 2000 17:30:56 -0400 From: Andrew T Pudzianowski Subject: Re: CCL:Molecular structure needed To: Dmitry Khoroshun Cc: chemistry@ccl.net Message-id: <39C14390.709E6D8A@bms.com> Organization: Bristol-Myers Squibb MIME-version: 1.0 X-Mailer: Mozilla 4.72 [en]C-BMY (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: <200009141931.PAA40998@euch4e.chem.emory.edu> Dmitry Khoroshun wrote: > Hello! > > Being a logical person, you may have taken a look at the rules of CCL > (although being totally abstract, your question *does* appear on CCL): > > http://www.ccl.net/chemistry/aboutccl/rules/ > > Particularly, at the lines: > > Unacceptable Topics > > Topics which may not appear on this list include: > > personal attacks > > topics unrelated to computational chemistry > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > It doesn't look like your question is obviously related to computational > chemistry. Does it to you? > > Sincerely, > Dmitry Khoroshun > dima@euch4e.chem.emory.edu > Fellow scientists and scholars - Experimental molecular structural data are indispensable to computational chemistry. We can, however, easily do without comments that border on personal attack, no matter how *politely* or *wittily* phrased they might be. Let's just keep those to ourselves and try to be helpful. Regards, Andrew Pudzianowski From chemistry-request@server.ccl.net Thu Sep 14 18:43:14 2000 Received: from socrates.cgl.ucsf.edu (socrates.cgl.ucsf.edu [128.218.27.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA26158 for ; Thu, 14 Sep 2000 18:43:14 -0400 Received: (from pak@localhost) by socrates.cgl.ucsf.edu (8.9.3/8.9.3/GSC1.7) id PAA397232 for chemistry@ccl.net; Thu, 14 Sep 2000 15:43:12 -0700 (PDT) Date: Thu, 14 Sep 2000 15:43:12 -0700 (PDT) From: Peter Kollman Message-Id: <200009142243.PAA397232@socrates.cgl.ucsf.edu> To: chemistry@ccl.net Subject: meeting announcement I just wanted to bring to everyone's attention, in case it was missed, that we are holding our 5th annual meeting at UCSF; all have been on subjects related to computational chemistry applied to biological molecules. Please come and let any interested colleagues know as well--as you can see from the program, it should be a very exciting meeting. peter kollman pak@cgl.ucsf.edu UCSF/MDI Symposium University of California San Francisco Department of Pharmaceutical Chemistry and Molecular Design Institute Symposium "Drug Design and Discovery" October 13-14, 2000 UCSF Laurel Heights Conference Center 3333 California Street San Francisco, CA 94118 SPEAKERS Johan Aqvist, Uppsala University Paul Anderson, Dupont Pharmaceuticals Ken Dill, University of California San Francisco Robert Fletterick, University of California San Francisco Simon Kearsley, Merck Research Laboratories Peter Kollman, University of California San Francisco Irwin Kuntz, University of California San Francisco Robert McDowell, Sunesis Jonathan Mason, Bristol Myers Squibb Kenneth Merz, Pharmacopeia David Pearlman, Vertex Pharmaceuticals Thomas Scanlan, University of California San Francisco Bruce Tidor, Massachusetts Institute of Technology Dennis Underwood, DuPont Pharmaceuticals Gennady Verkhivker, Agouron Pharmaceuticals For more information, please visit http://mdi.ucsf.edu or contact Kristina Clarke (tel: 415-514-0148; fax: 415-502-4690 or kristina@cgl.ucsf.edu