From kelterer@fptchbds01.tu-graz.ac.at Mon Feb 10 04:22:11 1997 Received: from fptchbds01.tu-graz.ac.at for kelterer@fptchbds01.tu-graz.ac.at by www.ccl.net (8.8.3/950822.1) id DAA09933; Mon, 10 Feb 1997 03:47:21 -0500 (EST) Received: by fptchbds01.tu-graz.ac.at (5.57/Ultrix3.0-C) id AA09455; Mon, 10 Feb 97 10:45:58 +0100 Date: Mon, 10 Feb 97 10:45:58 +0100 From: kelterer@fptchbds01.tu-graz.ac.at (M.Kelterer) Message-Id: <9702100945.AA09455@fptchbds01.tu-graz.ac.at> To: chemistry@www.ccl.net Subject: rir in MM3 Dear Netters, I have some unclear results with MM4(94): By calculating a system with a 5-ring I received sometimes "restricted internal rotation (rir) frequencies" i.e. characterised lower than 40/cm. But I did no-restriced motion input. So, it's not clear for me what quality of this minimum is. Sometimes I got also "free internal rotation (fir) frequencies" i.e. 0/cm (this was after a calculation by dihedral driver option or from an stochastic search), and if I made little changes in one dihedral angle, this became a saddle point. But the restricted frequencies remained restricted ones. Can someone help me with experience or some papers? Dr. Kelterer anne-Marie Technical University Graz, Austria e-mail: kelterer@fptchbds01.tu-graz.ac.at From Frederic.Bouyer@der.edfgdf.fr Mon Feb 10 05:22:09 1997 Received: from cf01 for Frederic.Bouyer@der.edfgdf.fr by www.ccl.net (8.8.3/950822.1) id EAA10203; Mon, 10 Feb 1997 04:50:29 -0500 (EST) Received: from clserv02.edf.fr (clserv02.edf.fr [130.98.118.118]) by cf01 (8.6.12/8.6.12) with ESMTP id KAA26339; Mon, 10 Feb 1997 10:55:27 +0100 Received: from ret45ab.der.edf.fr (ret45ab.der.edf.fr [192.196.125.12]) by clserv02.edf.fr (8.6.12/8.6.12) with ESMTP id KAA09317; Mon, 10 Feb 1997 10:50:06 +0100 Received: by ret45ab.der.edf.fr (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) id KAA00660; Mon, 10 Feb 1997 10:48:45 +0100 From: "Frederic Bouyer" Message-Id: <9702101048.ZM658@ret45ab.der.edf.fr> Date: Mon, 10 Feb 1997 10:48:43 +0100 In-Reply-To: Ning Xie "CCL:MnO4- & ZnCl2 complex" (Feb 8, 2:16am) References: X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Ning Xie Subject: Re: CCL:MnO4- & ZnCl2 complex Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, I would like to share experience on that point with people of the CCL. You can calculate HOMO/LUMO energies by any software you want. According to my personal experience, you could have some troubleshootings with the calculations of the HOMO/LUMO energies, you want to reproduce (keep in mind that the Koopman theorem is only valide for HF theory and not in the DFT context), with either adiabatic nor vertical estimations. Concerning the heat of formation, or some reaction energies you would compute, I had some trouble to reproduce reaction energies involving anions (with DFT methodologies and HF + MP2 even if **diffuse** functions were taken into account!). So to my experience, I would recommend to calculate reaction energies for **neutral** molecules/complexes. Could I recommend to study for instance KMnO4 (its heat of formation), and to growth the system, to see what is the effect of the solvent -aqueous or molten salt- (and increase the size the sphere solvation, if you can: this can be seen as structural rearrangements of atoms within a small system ...). This methodology gave me in the past very good prediction. Hope this will help you. Frederic Bouyer From schmitt@chemie.uni-wuerzburg.de Mon Feb 10 05:31:23 1997 Received: from wrzx01.rz.uni-wuerzburg.de for schmitt@chemie.uni-wuerzburg.de by www.ccl.net (8.8.3/950822.1) id FAA10282; Mon, 10 Feb 1997 05:09:40 -0500 (EST) Received: from wocx04.chemie.uni-wuerzburg.de by wrzx01.rz.uni-wuerzburg.de (4.1/uniwue-M-3.2) id AA08951; Mon, 10 Feb 97 11:09:40 +0100 Received: by wocx04.chemie.uni-wuerzburg.de (931110.SGI/uniwue-C-3.0) id AA12864; Mon, 10 Feb 97 11:06:47 +0100 Date: Mon, 10 Feb 1997 11:06:46 +0100 (MET) From: Stefan Schmitt To: chemistry@www.ccl.net Subject: CoMFA with racemic compunds? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Computer Chemists, stereo I am doing 3D-QSAR analysis using SYBYL's standard QSAR module from Tripos. The compounds I am analyzing contain one (and for some derivatives two) stereogenic center(s). Biological data (IC50) however, is due to experimental reasons only availible for racemic mixtures (or diastereomeric mixtures in the case of two stereogenic centers). My question is now, how to handle this information for a CoMFAnalysis: Is it right to use both isomeric structures as CoMFA-input and give them the same activity? It may sound logical but I am not aware if such a proceeding would falsify the input for the PLS-analysis. Alternatively you could use only one isomeric structure, but this would not truely reflect the right 3D-demands at the receptor. I am thankful for any information or ideas on this problem. Cheers! ======================================================= ---- -- -// / // -- --// Stefan Schmitt cand. chem. / // --- --- // Universitaet Wuerzburg / // // Institut fuer Organische Chemie / // - -- // AK Prof. Dr. G. Bringmann / // // Computational Chemistry Group / // --- // / // // Am Hubland / // - // 97074 Wuerzburg / // // Germany / // //____________________________________________________ // // // // e-mail : schmitt@chemie.uni-wuerzburg.de // // voice : (0049)-(0)-931-888-4750 // // fax : (0049)-(0)-931-888-4755 // // // ======================================================== From peon@medchem.dfh.dk Mon Feb 10 06:22:24 1997 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id FAA10456; Mon, 10 Feb 1997 05:31:46 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id LAA22080; Mon, 10 Feb 1997 11:30:31 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id MAA10465; Mon, 10 Feb 1997 12:06:31 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 10 Feb 1997 11:30:31 +0100 To: kelterer@fptchbds01.tu-graz.ac.at (M.Kelterer) From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:rir in MM3 Cc: chemistry@www.ccl.net Dr. Kelterer asked: >Dear Netters, >I have some unclear results with MM4(94): >By calculating a system with a 5-ring I received >sometimes "restricted internal rotation (rir) frequencies" >i.e. characterised lower than 40/cm. But I did no-restriced >motion input. So, it's not clear for me what quality of this >minimum is. >Sometimes I got also "free internal rotation (fir) frequencies" >i.e. 0/cm (this was after a calculation by dihedral driver option >or from an stochastic search), and if I made little changes in one >dihedral angle, this became a saddle point. >But the restricted frequencies remained restricted ones. >Can someone help me with experience or some papers? The terms "restricted" and "free" in the above output may be a little confusing, they don't refer to the way the calculation was run, but rather is a simplified diagnostic. What it tells you is simply that you cannot trust the thermodynamic corrections when you have "restricted internal rotation (rir) frequencies" in the calculation. The minimum is good though, as long as you only want to use it for verifying stationary points, you're OK. My guess is that you shouldn't use the frequency calculation with dihedral driver (I'm using MM3(92), I thought they were incompatible). When you are using dihedral driver, you're almost certain to end with a structure which is not a true minimum, just a restricted one. In this case, the frequency analysis has no meaning. I'm not sure if MM3(94) has the ability to project out the forces due to the restrained dihedral (it does seem that way if you can run it), in that case the calculation might be good for verifying that the structure is a stationary point with respect to the remaining degrees of freedom, but I'm on shaky ground here, I don't really know what is allowed or not. Anybody else? Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From bmichael@techunix.technion.ac.il Mon Feb 10 11:22:16 1997 Received: from techunix.technion.ac.il for bmichael@techunix.technion.ac.il by www.ccl.net (8.8.3/950822.1) id KAA24538; Mon, 10 Feb 1997 10:58:15 -0500 (EST) Received: from localhost (bmichael@localhost) by techunix.technion.ac.il (8.8.5/8.6.10) with SMTP id RAA01301 for ; Mon, 10 Feb 1997 17:57:56 +0200 (IST) Date: Mon, 10 Feb 1997 17:57:55 +0200 (IST) From: Michael Bendikov To: chemistry@www.ccl.net Subject: Model potential for electronic structure of clusters. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody ! Are you aware of any electronic structure computations of A \sub n clusters involving simple (local, energy independent) model potentials leading to a qualitatively correct electronic energy levels (Na \sub n can serve as a good example). By a qualitative correctness I mean approximately correct single ionization energy + approximately correct energies of singly excited configurations. If you are aware of similar calculations of band structure of solids or thin films based on cluster model + all of the above, please, respond too. I will summarize the answers. E-mail: bmichael@tx.technion.ac.il Thank you in advance, Michael Bendikov From bear@ellington.Pharmacy.arizona.edu Mon Feb 10 13:22:15 1997 Received: from ellington.Pharmacy.arizona.edu for bear@ellington.Pharmacy.arizona.edu by www.ccl.net (8.8.3/950822.1) id MAA05448; Mon, 10 Feb 1997 12:41:56 -0500 (EST) Received: (from bear@localhost) by ellington.Pharmacy.arizona.edu (8.8.5/8.8.5) id KAA03464 for chemistry@www.ccl.net; Mon, 10 Feb 1997 10:41:56 -0700 (MST) Date: Mon, 10 Feb 1997 10:41:56 -0700 (MST) From: Soaring Bear Message-Id: <199702101741.KAA03464@ellington.Pharmacy.arizona.edu> To: chemistry@www.ccl.net Subject: Re: CCL:CoMFA with racemic compunds? >Is it right to use both isomeric structures as CoMFA-input and give them the >same activity? The greater the difference of real activity of each of the isomers the greater the error will be in prediction. It just adds another unknown so should be avoided. Better to leave those compounds out.  ___ _ http://ellington.pharm.arizona.edu/~bear O-topo-O (___ |.) bear@ellington.pharm.arizona.edu 5' : : .* ___)OARING |_)EAR, UA Pharmacy 404, Tucson 85721 |'*. .*'| | Computer Modeling for Medicinal Chemistry; SAR CAMD | | *.,* | | | Protein/DNA Structural Biology; Cancer Biochemistry 3',DNA helix|.* Pharmacognosy, Herbs, Nutrition, Natural Dentistry '***' '**  From Alan.Shusterman@directory.Reed.EDU Mon Feb 10 13:47:50 1997 Received: from reed.edu for Alan.Shusterman@directory.Reed.EDU by www.ccl.net (8.8.3/950822.1) id NAA05796; Mon, 10 Feb 1997 13:19:56 -0500 (EST) Received: from isis.Reed.EDU [134.10.2.1 no identification] by reed.edu (/\oo/\ Smail3.1.29.1osf1 #29.2) id ; Mon, 10 Feb 97 10:19 PST Message-id: <2536658@isis.Reed.EDU> Date: 10 Feb 97 10:19:40 PST From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) Subject: Re: CCL:CoMFA with racemic compunds? To: chemistry@www.ccl.net --- Stefan Schmitt wrote: The compounds I am analyzing contain one (and for some derivatives two) stereogenic center(s). Biological data (IC50) however, is due to experimental reasons only availible for racemic mixtures (or diastereomeric mixtures in the case of two stereogenic centers). My question is now, how to handle this information for a CoMFAnalysis: Is it right to use both isomeric structures as CoMFA-input and give them the same activity? It may sound logical but I am not aware if such a proceeding would falsify the input for the PLS-analysis. Alternatively you could use only one isomeric structure, but this would not truely reflect the right 3D-demands at the receptor. --- end of quoted material --- This looks like a difficult problem. You should never assume that the enantiomers have the same biological activity (occasionally they do, but there are many many cases where they do not). It may also be unsafe to assume similar receptor interactions for each enantiomer, but this will depend on the structure of the molecule and the mechanism of receptor binding. Assigning the same activity to both isomers and proceeding with the CoMFA and PLS analysis will definitely invalidate the results unless the activities of the isomers are, in fact, similar. What might be worth a try is to choose one enantiomer in each pair as the more active molecule and to assign all of the measured activity to this molecule. Then, include only this molecule in the CoMFA analysis and discard the other (until more data becomes available). Alan Shusterman Department of Chemistry Reed College Portland, OR From jkl@ccl.net Mon Feb 10 14:22:22 1997 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.8.3/950822.1) id NAA05949; Mon, 10 Feb 1997 13:38:24 -0500 (EST) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.3/950822.1) id NAA08411; Mon, 10 Feb 1997 13:38:20 -0500 (EST) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id NAA12653; Mon, 10 Feb 1997 13:38:16 -0500 (EST) Date: Mon, 10 Feb 1997 13:38:16 -0500 (EST) Message-Id: <199702101838.NAA12653@krakow.ccl.net> To: chemistry@www.ccl.net Subject: QCPE Info & Catalog available in CCL Archives Cc: jkl@ccl.net, qcpe@indiana.edu Dear Netters, In coorperation with Quantum Chemistry Program Exchange (QCPE) we are placing the catalog and other QCPE information in the archives of Computational Chemistry List: http://www.ccl.net/ccl/qcpe (you can also get there via CCL home page: http://www.ccl.net/chemisty.html). These pages contain a lot of information about programs, methods, as well as, algorithms of computational chemistry. The information is also searchable together with the rest of the CCL archives. Please enjoy... And join us in thanking Dr. Counts for the opportunity to have this information in the Web format. If you notice some glitches please let us know. We admit that most of the conversion was done with scripts, and we were not able to check each and every page (there are about 1700 Web pages in this collection). So your help will be greatly appreciated. Jan Labanowski jkl@ccl.net From andy@neptune.chem.uga.edu Mon Feb 10 14:25:31 1997 Received: from neptune.chem.uga.edu for andy@neptune.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id NAA05827; Mon, 10 Feb 1997 13:23:02 -0500 (EST) Received: (from andy@localhost) by neptune.chem.uga.edu (8.7.4/8.7.3) id NAA13411; Mon, 10 Feb 1997 13:23:34 -0500 Date: Mon, 10 Feb 1997 13:23:30 -0500 (EST) From: Andy Dustman Sender: andy@neptune.chem.uga.edu To: Per-Ola Norrby cc: "M.Kelterer" , chemistry@www.ccl.net Subject: Re: CCL:rir in MM3 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 10 Feb 1997, Per-Ola Norrby wrote: > My guess is that you shouldn't use the frequency calculation with > dihedral driver (I'm using MM3(92), I thought they were incompatible). > When you are using dihedral driver, you're almost certain to end with a > structure which is not a true minimum, just a restricted one. In this > case, the frequency analysis has no meaning. I'm not sure if MM3(94) has > the ability to project out the forces due to the restrained dihedral (it > does seem that way if you can run it), in that case the calculation might > be good for verifying that the structure is a stationary point with respect > to the remaining degrees of freedom, but I'm on shaky ground here, I don't > really know what is allowed or not. Anybody else? When you use the dihedral driver, you need to use block diagonal Newton-Raphson minimization, not full Newton-Raphson. The latter mode is necessary for vibrational calculations. You can, however, use the torsion driver to drive over an energy barrier and THEN use full Newton-Raphson on that conformation to find a transition state. -- Andy Dustman / Computational Center for Molecular Structure and Design / UGA You can have my PGP public key by sending mail with subject "send file key". You can have my PGP secret key when you pry it out of my cold, dead neurons. http://charon.chem.uga.edu/~andy mailto:andy@CCMSD.chem.uga.edu <}+++<