Shape-filling molecular models

In the case of 3D space-filled molecular models, one can represent the molecule by contour profiles, which are shape profiles calculated for all individual contours used to map the molecule. Each contour profile is then defined by a sequence ... 

Top Each molecule consists of eight S atoms arranged in a ring (in the shape of a crown). Bottom Space-filling molecular model. 

As useful as molecular models are, they are limited in that they only show the location of the atoms and the space they occupy. Another important dimension to molecular structure is its electron distribution. We introduced electrostatic potential maps in Section 1.5 as a way of illustrating charge distribution and will continue to use them throughout the text. Figure 1.6(d) shows the electrostatic potential map of methane. Its overall shape is similar to the volume occupied by the space-filling model. The most electron-rich regions are closer to carbon and the most electron-poor ones are closer to the hydrogens. 

A molecule is a three-dimensional array of atoms. In fact, many of a molecule s properties, such as its odor and chemical reactivity, depend on its three-dimensional shape. Although molecular and structural formulas describe the composition of a molecule, they do not represent the molecule s shape. To provide information about shapes, chemists frequently use ball-and-stick models or space-filling models. 

A different density surface (0.002 electrons/au ) serves to portray overall molecular size and shape. This is, of course, the same information portrayed by a conventional space-filling (CPK) model. ... 

The traditional way to represent a molecular structure is illustrated by the space-filling model in Figure 2 the ball-and-stick model is another. By a process of supermagnification, such iconic models26 bring the unseen molecule into the familiar world of everyday experience An object with a distinct shape that we can relate to, that we can handle, see, and enjoy. Indeed, the metaphor molecular shape works amazingly well It encapsulates and conveys a great deal of useful chemical information, it is of undeniable heuristic and didactic value, and it serves as a powerful fount of inspiration.27 In this way the molecular property that we call chirality becomes a vivid reality when we examine molecular models of enantiomers. But certain approximations are needed to yield this familiar picture of a molecule, that is, the classical model, and these need to be discussed next. 

Figure IIB. A space-filling representation of the framework drawing of psilocin depicted in Figure llA. The molecular structures depicted in the figures in this chapter are two-dimensional, line-drawing representations of the molecules that show how the atoms are connected and allow for ready comparison of similarity between molecules. Molecules actually have three-dimensional shapes in which each of the constituent atoms occupies a volume defined by its cloud of electrons. Linus Pauling and two of his colleagues, Robert Corey and Walter Koltun, first developed a form of molecular models to depict the 3-dimensional space-filling aspect of molecules in the way shown in this figure.

Since compounds of carbon are held together chiefly by covalent bonds, organic chemistry, too, is much concerned with molecular size and shape. To help us in our study, we should make frequent use of molecular models. Figure 1.11 shows methane as represented by three different kinds of models stick-and-ball, framework, and space-filling. These last are made to scale, and reflect accurately not only bond angles but also relative lengths of bonds and sizes of atoms. 

The solution to any problem with a stereochemical aspect requires access to molecular models. Of these, there are two main kinds. The first is the skeletal or framework model such as those devised by Dreiding or Kendrew. These indicate the centres of bonds that join atoms, and are useful to find conformations suitable for interaction between two molecules. The other type of model, space-filling (e.g. CPK, or Courtauld), shows both the shape of the molecule and the volume that it occupies. This kind is very useful for showing the overall shape, surface and volume of a molecule. With practice, a chemist can learn to see a conformational drawing as a three-dimensional skeletal shape, and eventually as a space-filling molecule. There are also the CCS models, which are fundamentally skeletal models that can be quickly converted to space-filling types and back again (Clarke, 1977). 

Figure 13. Energy-minimized molecular model of the saponin hydrolyzate from Panax notoginseng top two views of the tube model without hydrogen atoms for clarity bottom space-filling model giving the shape (H white C black 0 gray).

Energy-minimized molecular modeling based on the stereostructure found by X-ray crystallography or spectroscopic elucidation provides the best means of obtaining the shape of molecules by using space-filling models, as demonstrated for three monoterpenes in Fig. 14. 

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