From chemistry-request@server.ccl.net Sat Aug 5 06:17:11 2000 Received: from backmail.mahidol.ac.th (backmail.mahidol.ac.th [202.28.162.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA08876 for ; Sat, 5 Aug 2000 06:16:55 -0400 Received: from mucc.mahidol.ac.th (IDENT:sctkc@mucc.mahidol.ac.th [202.28.162.1]) by backmail.mahidol.ac.th (8.10.0/8.10.0) with ESMTP id e75AIuU28689; Sat, 5 Aug 2000 17:18:57 +0700 (GMT+0700) Received: from localhost (sctkc@localhost) by mucc.mahidol.ac.th (8.9.3/8.9.3) with SMTP id RAA26692; Sat, 5 Aug 2000 17:15:46 +0700 (GMT+0700) Date: Sat, 5 Aug 2000 17:15:46 +0700 (GMT+0700) From: Teerakiat Kerdcharoen To: "Shobe, Dave" cc: "'CCL'" Subject: Re: CCL:TM force fields - questions In-Reply-To: <157A51F55AAAD3119CD70008C7B1629D638462@lvlxch01.unitedcatalysts.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I partly agree that it is possible to implement more sophisticated MM force field to represent TM-Ligand interactions and if you look back to 1990 and before there have been a lot of efforts to model these stuffs. My point is that much efforts have been done but less results and success have been achieved. Current attempts therefore lies hope with something like QM/MM method. You don't need to model the chemistry of difficult thing with classical mechanics like MM, instead do it with quantum mechanics. In such aspect, less efforts have been done but surpringly with great results. take care, Teerakiat On Thu, 3 Aug 2000, Shobe, Dave wrote: > I'm not an expert in molecular mechanics, but I've been following this > discussion and here's my $.02: > > The fact that M-L1 bond lengths vary according to the identity and placement > of the other ligands does not mean that molecular mechanics (MM) is > impossible for transiton metal complexes, only that a decent > parameterization would be much more complicated than for p-block elements. > It may mean that MM software that was designed for organic molecules will be > unable to accurately predict metal complex geometries without major > revisions--that it's not just a matter of defining parameters for new atom > types, since the factors influencing the geometry are quite different. On > the other hand, even from a "pure science" point of view, I think that a > decent MM algorithm/parameterization for transition metal complexes would be > a worthwhile and interesting goal. ------------------------------------------------------------------------ Teerakiat Kerdcharoen, Ph.D. Profession: University Lecturer Address: Department of Physics, Faculty of Science Mahidol University, Bangkok 10400 Office Phone: (66)(2) 2461381 FAX (66)(2) 2461381 Home Phone: (66)(2) 5893099 FAX (66)(2) 9547395 Mobile: (66)(2) 9548083 and press 1 (PCT) (66)(1) 8023236 (GSM) Homepage: http://einstein.sc.mahidol.ac.th/teerakiat Research: Computer Simulation / Computational Nanotechnology ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Sat Aug 5 00:21:18 2000 Received: from imo-r11.mx.aol.com (imo-r11.mx.aol.com [152.163.225.65]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA07554 for ; Sat, 5 Aug 2000 00:21:18 -0400 From: AMSales12@aol.com Received: from AMSales12@aol.com by imo-r11.mx.aol.com (mail_out_v27.12.) id g.50.91cf6bc (7381) for ; Sat, 5 Aug 2000 00:19:09 -0400 (EDT) Message-ID: <50.91cf6bc.26bcefbc@aol.com> Date: Sat, 5 Aug 2000 00:19:08 EDT Subject: Galaxy 2.9 To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: AOL 5.0 for Windows sub 112 AM Technologies Inc., is glad to announce the availability of a demo version of their multipurpose molecular modeling software package, Galaxy-2.9. It has everything that you need for drug discovery and molecular simulation. An SGI version may be down loaded after signing our Guest Book. A fully functional copy with a 90-days license can be down loaded after paying $500.00. We also have an excellent offer for the academic institutes. Please check our WebPages (http://www.am-tech.com/) for the detail information. From chemistry-request@server.ccl.net Sat Aug 5 00:56:18 2000 Received: from mail4.nycap.rr.com (mail4-1.nyroc.rr.com [24.92.33.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA07665 for ; Sat, 5 Aug 2000 00:56:18 -0400 Received: from claessenhome.nycap.rr.com ([24.161.16.32]) by mail4.nycap.rr.com (Post.Office MTA v3.5.3 release 223 ID# 0-59787U250000L250000S0V35) with SMTP id com for ; Sat, 5 Aug 2000 00:59:48 -0400 Reply-To: From: "Rolf Claessen" To: "CCL" Subject: Protein Modeling Software for RS6000? Date: Sat, 5 Aug 2000 00:55:17 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal In-Reply-To: <000d01bffe20$e5e40dc0$9b037b81@chem.usu.edu> X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Colleagues, I am looking for protein/peptide modeling software for the RS6000 computer running AIX. Polymer modeling capability would be a plus. Any recommendations? Regards, Rolf Claessen http://www.claessen.net From chemistry-request@server.ccl.net Sat Aug 5 08:12:10 2000 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA10229 for ; Sat, 5 Aug 2000 08:12:09 -0400 Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by mserv.rug.ac.be (8.9.3/8.9.3) with ESMTP id OAA05309; Sat, 5 Aug 2000 14:11:56 +0200 (MET DST) Received: (from patrick@localhost) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) id OAA09778; Sat, 5 Aug 2000 14:16:07 +0100 (NFT) Date: Sat, 5 Aug 2000 14:16:07 +0100 (NFT) From: Patrick Bultinck To: chemistry@ccl.net, robert.latour@ces.clemson.edu Subject: mixing entropies for a molecule with multiple minima (corr.) Message-ID: 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 IAA10230 Dear all, There has been a little confusion on the question I raised, because I jumped to DS° calculations too rapidly (some DX° notations should have been X°). So here is the corrected version : >I would like to calculate thermodynamical parameters (H°, S° >and G°) for an ensemble of conformations of a molecule. H° etc. can >easily be calculated for each conformation by calculating the hessian. G° >is also easily calculated of course. Using Boltzmann's law, one can >calculate the mole fractions of each conformation you would have for one >mole of the molecule. H° is easily calculated for the ensemble using the >individual mole fractions and H° values for each conformation. S° also in >first approximation, but... should S° not be augmented with a mixing >entropy term because you are mixing different conformations, which you all >treat separately as ideal gases ? I think you would need to add a term >S°(mix)=sum(x_i*ln(x_i)), where x_i is the mole fraction for conformation >i. Since you treat them as ideal gases, nothing changes in H° for the >ensemble (they do not interact). Using the mixing-corrected S°, a new G° >can be calculated. > >So I am using the following steps to calculate G° for an ensemble of >conformations of the same molecule : >- Calculate H°, S° and G° for each conformation separately >- Correct where necessary for chiral degeneracy of each conformation, and >obtain (for some conformations) chiral corrected values (not every ab >initio program does this on the fly). >- Calculate Boltzmann determined occupations for all conformations. >- Calculate H° for the ensemble of conformations, as well as S° from >individual H° and S° values of all conformations >- Correct S° with a mixing term, accounting for the fact that each >conformation is an ideal gas, and that mixing ideal gases brings about a >mixing entropy. >- Calculate a new G° value from H° and the corrected S° value. > >In my opinion, only then can I calculate the DG° value in a reaction : >metal + ligand -> complex. > >I would very much appreciate your opinions on this. I am not ignorant in >thermodynamics, but I would like to have more experienced people to comment >on my way to calculate G° for an ensemble of conformations of the same >molecule. Especially for the fact that Boltzmann is used to calculate mole >fractions for each conformation, based on individual values for each >conformation, and that then later on, a term is added to S° which can only >be calculated for an ensemble (but to calculate S_mix, you need the mole >fractions first)... > >I think the method I suggest might be correct, since not including S(mix) terms for the ligand in two reactions sometimes yields crazy results, e.g. entropically more favourable formation of 6-membered ring complex than a 5-membered ring complex starting from two different chelating ligands (ethylenediamine and 1,3-propanediamine). >Thanks, > >Patrick Bultinck >Ghent University >Belgium