Subject: Re: CCL:Question about CERIUS 2

From: Michael Doyle <[email-masked]>
Date: Thu, 21 May 1998 17:18:51 -0700

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

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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).

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Michael Doyle @ MSI

Materials Informatics and QSAR 

Product Manager

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WRK</bold> 619-546-5358

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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!

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<bold><color><param>ffff,0000,0000</param><bigger>The opinions expressed
here are solely those of 

Michael J. Doyle and do not reflect those of MSI
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