H.W. Gibson
Rotaxane is a compound which consists of a cyclic molecule which is threaded by a linear molecule; there is no covalent bond between the two species. The name derives from the Latin words for wheel and axle. Polymeric analogs of these small compounds can consist of very long linear species and have a very large number of cyclic molecules threaded along the backbone. Alternatively the cyclic species may be incorporated into the polymeric backbone or included as a group pendant from the backbone and can be threaded by either low molecular weight or high molecular weight linear species. The synthesis of this new class of materials has been pioneered in our group by using simulation-visualization resources on campus. The proposed CAVE environment linked with other computational resources on campus would constitute a significant improvement on the present simulation-visualization resources.
It is well known in polymer science that the molecular shapes of species with the same chemical constitution play a very critical role in the determination of physical properties. For example the viscosity in solution and melt states, which depends upon the interaction of the macromolecule with the surroundings, is very sensitive to shape. Solid state properties, such as the glass transition temperature, the melting point, indeed, even the presence of crystalline order, and mechanical behavior, which depend upon packing in a matrix, are also responsive to molecular shape. From a general experimental perspective then it is well appreciated that changes in molecular geometry or topology play a significant role in physical properties in both solution and solid states of polymeric materials.
Polyrotaxanes challenge our fundamental understanding of these relationships. The details of the 3-dimensional organization of the systems and the response of the structures to changes in environment are poorly understood on a molecular our ability to predict the physical properties is limited. The objective of this project is to develop a sufficient understanding of the structures and interactions in polyrotaxanes to be able to predict physical properties of importance in the solution, molten and solid states. These calculations involve extensive computation because there are many atoms, many rotatatable bonds and a very large number of conformational states. The ability to visualize simulation results is used to develop predictive capabilities, hence this research would particulary benefit from access to a 3D visualization CAVE environment.
All of these simulation-visualization activities are computationally intensive because of the sizes of the polyrotaxanes and the necessity of examining a large number of structures as a function of simulated thermal and mechanical stresses in order to predict bulk properties with any confidence.
We currently employ a variety of commercial programs to attack this problem at various levels. In particular we use Molecular Simulations' Polygraf and Cerius with AVS. With these 3D simulation- visualization tools we will develop first on our desktop workstations and then thes same tools can take advantage of the unique CAVE environment where there is advantage to be immersed in particularly complex 3D structures.