Three Dimensional Molecular Modelling

Integration of Three-dimensional Substructure Searching and Molecular Modeling Three-dimensional Similarity Searching... 

When di.scivssing molecular orbitals, three-dimensional models or visualization software may be very instrustive. 

Several research groups have built models using theoretical desaiptors calculated only from the molecular structure. This approach has been proven to be particularly successful for the prediction of solubility without the need for descriptors of experimental data. Thus, it is also suitable for virtual data screening and library design. The descriptors include 2D (two-dimensional, or topological) descriptors, and 3D (three-dimensional, or geometric) descriptors, as well as electronic descriptors. 

The ball and wire display is used for model building Although it is convenient for this purpose other model displays show three dimensional molecular structure more clearly and may be preferred The space filling display is unique m that it portrays a molecule as a set of atom centered spheres The individual sphere radii are taken from experi mental data and roughly correspond to the size of atomic electron clouds Thus the space filling display attempts to show how much space a molecule takes up... 

Protein Data Bank (Section 27 20) A central repository in which crystallographic coordinates for biological mole cules especially proteins are stored The data are accessi ble via the Worldwide Web and can be transformed into three dimensional images with appropriate molecular modeling software... 

Fig. 7. Model for PVC fusion, accounting for molecular weight effects and processing temperature effects (a) unfused PVC primary particles (b) partially melted PVC primary particles (c) partially melted then recrysta11i2ed high molecular weight PVC, showing strong three-dimensional stmcture and (d) partially melted then recrysta11i2ed low molecular weight PVC, showing weak three-dimensional stmcture.

Three-Dimensional Modeling of Chemical Structures. The two-dimensional representations of chemical stmctures are necessary to depict chemical species, but have limited utiHty in providing tme understanding of the effects of the three-dimensional molecule on properties and reactive behavior. To better describe chemical behavior, molecular modeling tools that reflect the spatial nature of a given compound are required. 

Early efforts to develop molecular models emphasized ways of representing three-dimensional aspects in two-dimensional projections. Some of the problems addressed were the folding of macromolecules (43,44) and two-dimensional projections with hidden surfaces (45,46). The state of the art in the early 1970s has been reviewed (47). 

It is somewhat difficult conceptually to explain the recoverable high elasticity of these materials in terms of flexible polymer chains cross-linked into an open network structure as commonly envisaged for conventionally vulcanised rubbers. It is probably better to consider the deformation behaviour on a macro, rather than molecular, scale. One such model would envisage a three-dimensional mesh of polypropylene with elastomeric domains embedded within. On application of a stress both the open network of the hard phase and the elastomeric domains will be capable of deformation. On release of the stress, the cross-linked rubbery domains will try to recover their original shape and hence result in recovery from deformation of the blended object. 

Draw three-dimensional representations or make molecular models of... 

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