From mdoyle: at :msi.com Thu May 21 20:21:44 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id UAA07650 Thu, 21 May 1998 20:21:43 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry %-% at %-% www.ccl.net id AA28501; Thu, 21 May 98 17:18:52 -0700 Received: from mdoyle-pc.msi.com(146.202.24.32) by bioc1.msi.com via smap (V2.0) id xmag28472; Thu, 21 May 98 17:18:25 -0700 Message-Id: <3.0.32.19980521170618.006d78b8 -8 at 8- 146.202.6.217> X-Sender: mdoyle $#at#$ 146.202.6.217 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 21 May 1998 17:18:51 -0700 From: Michael Doyle Subject: Re: CCL:Question about CERIUS 2 To: "'CCL'" Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Dear CCLers, Derick and David, The free volume calculations is part of the specialist polymer analysis tools and does not form a direct part of the C2 QSAR and C2-Descriptor+ sets. It is however a set of information that using the C2SDk can be passed into the QSAR tables. MICHAEL -----------------------------------------------------------------------------------------\-- Free volume analysis using Voronoi tessellation The model is subdivided into space filling complex polyhedra surrounding each atom. Each polyhedron can be thought of as encompassing the volume "belonging" to that atom. The tesselation process can be more easily visualized in 2D. A line is drawn between each pair of atoms and a plane is placed normal to the line at its center (shown as a solid line). As the planes intersect they produce a polyhedra. The tesselation results give much more information than the simple measures of total, occupiable and unoccupiable free volume. The distribution of hole sizes and the shapes of the holes (the surface area/volume ratio = (S/4)/(3V/4) where S and V refer to the polyhedron surface area and volume, it has a minimum value of 1.0 for a sphere) are likely to correlate with properties involving molecular packing. By selecting the atoms used for the tesselation the free volume associated with different parts of the system can be studied. For example: free volume around chain ends verses chain center to look at molecular weight effects (ref), free volume around additives such as plasticizers, etc. References: Ferry, J. D. "Viscoelastic Properties of Polymers" John Wiley & sons, New York (1980) D. Rigby and R. J. Roe, "Molecular Dynamics Simulation of Polymer Liquid and Glass 4. Free Volume Distribution" Gusev, A. A.; Suter, U. W. "Dynamics of small molecules in dense polymers subject to thermal motion" J. Chem. Phys., 99, 2228 (1993). Gusev, A. A.; Arizzi, S.; Suter, U. W.; Moll, D. J. "Dynamics of light gases in rigid matrices of dense polymers" J. Chem. Phys., 99, 2221 (1993). Gusev, A. A.; Muller-Plathe, F.; van Gunsteren, W. F.; Suter, U. W. "Dynamics of small molecules in bulk polymers" in Atomistic Modeling of Physical Properties, Adv. Polym. Sci., 116, 207 (1994).
ffff,0000,0000 -=-=-=-=-=-=-=-=-=-=-=- 0000,0000,ffff-=-=-=-=-=-=-=-=-=-=-=- Michael Doyle ":at:" MSI Materials Informatics and QSAR Product Manager WRK 619-546-5358 FAX 619-458-0136 HME 760-471-2910 (VOX&FAX) CAR 760-809-1225 WEB www.msi.com ffff,0000,0000-=-=-=-=-=-=-=-=-=-=-=- 0000,0000,ffff-=-=-=-=-=-=-=-=-=-=-=- ffff,0000,0000 ffff,0000,0000 Technology that was available to expert modelers for thousands of dollars a few years ago is now available to all research scientists for under five hundred dollars! Go get a copy for yourself before you are left behind! Check out 0000,0000,fefehttp://www.msi.com/weblab/viewer/info/index.shtml ffff,0000,0000The opinions expressed here are solely those of Michael J. Doyle and do not reflect those of MSI Inc.