From owner-chemistry@ccl.net Sat Oct 6 08:08:01 2007 From: "Arvydas Tamulis tamulis(~)mserv.itpa.lt" To: CCL Subject: CCL: PVED of D- and L-serine molecules Message-Id: <-35336-071006072419-4410-+lF2LP0yYsqgWnez8hTc8Q- -server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Sat, 6 Oct 2007 14:23:58 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis{=}mserv.itpa.lt] Dear Flick, thank you very much for your advises. Let say You or Others, Do I am right with my further planing work: I will take coordinates of my obtained enantiomer with lowest total energy, then invert coordinates and once again reoptimize geometry of these two D- and L-serine molecules, and continue this procedure until I will get the same rotomer geometry for each D- and L-serine molecules (until the total energies of D- and L-serine molecules will be exactly the same. After obtaining the D- and L-serine molecules with the exactly the same geometry, I am planing to apply to DIRAC relativistic package for the obtaining the PVED of D- and L-serine molecules. Maybe somebody else already done these PVED calculations of D- and L-amino acids molecules with DIRAC or other packages and can advise me with all other problems during this research? Cheers, Arvydas On Fri, 5 Oct 2007, William F. Coleman wcoleman+/-wellesley.edu wrote: > > Sent to CCL by: "William F. Coleman" [wcoleman===wellesley.edu] > One way to invert stereochemistry is with the free DSV Visualizer > (http://www.accelrys.com/products/downloads/ds_visualizer/index.html). > GaussView 4 will also do this, they say, but I haven't received ours yet. > > I would take one isomer, minimize it using the desired model chemistry, > and then invert it and calculate the energy of the other isomer. Even > with something as simple as serine there will be many local minima arising >> from rotations about the OH, NH2 and carboxyl groups that producing an > exact mirror image by optimization of two independently drawn structures > will be a low probability event. > > Cheers, > > Flick > > _______________ > William F. Coleman > Professor of Chemistry > Wellesley College > Wellesley MA 02481 > > on leave 2007-08 - please contact via email only > wcoleman##wellesley.edu > > www.wellesley.edu/Chemistry/colemanw.html > > Editor, JCE WebWare and JCE Featured Molecules > http://www.jce.divched.org/JCEDLib/WebWare/ > http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html> > > From owner-chemistry@ccl.net Sat Oct 6 14:25:00 2007 From: "Alexandre Hocquet alexandre.hocquet%ensic.inpl-nancy.fr" To: CCL Subject: CCL: Quantitative measure for susceptibility to nucleophilic attack Message-Id: <-35337-071005114621-14769-i9OKTMeMop7+Q38KC5/xaA##server.ccl.net> X-Original-From: "Alexandre Hocquet" Date: Fri, 5 Oct 2007 11:46:17 -0400 Sent to CCL by: "Alexandre Hocquet" [alexandre.hocquet * ensic.inpl-nancy.fr] >> I am interested in techniques which can provide a measure of >> susceptibility to nucleophilic attack in a particular fragment across >> a series of molecules. The goal is to have a quantitative measure of >> how different substitutents at another site affect the likelihood of >> nucleophilic attack at the site of interest. >> >> This is somewhat removed from the areas of electronic structure to >> which I am accustomed. I understand from reading Bader's book that >> divots and bumps in the lapacian of the density can be an indication >> of these, but I was wondering if there was something a little more >> straightforward to analyze. >> >> Can anyone point me to some references? In addition to the the work of Senet, you may want to have a look at this paper : Conceptual Density Functional Theory P. Geerlings,* F. De Proft, and W. Langenaeker Chem. Rev., 103 (5), 1793 -1874, 2003 It presents the framework of conceptual dft, a paradigm where you can surely find tools to calculate what you need. One of these tools, the dual descriptor, can map quantitatively the nucleophilic and electrophilic regions within a molecule. it has been presented in this paper : Morell, C.; Grand, A.; Toro-Labb, A. J. Phys.Chem. A 2005, 109,205 Yours, -- *********************************************** Alexandre Hocquet Ecole Europenne d'Ingnieurs en Gnie des Matriaux 6, rue Bastien Lepage 54010 Nancy Cedex Alexandre.Hocquet-x-eeigm.inpl-nancy.fr http://www.eeigm.inpl-nancy.fr/~hocque23/ ***********************************************