Space-filling molecular model

Chemists use both chemical names and molecular pictures to describe molecules. Molecular pictures take several forms, including structural formulas, ball-and-stick models, space-filling models, and line structures. These molecular representations can help you improve your ability to think molecules. ... 

Molecular formula Structural formula Ball-and-stick model Space-filling model... 

Molecular models (ball and stick models, space-filling models) which reproduce typical bond lengths and bond angels and hence stereochemical and congestional effects. However, certain aspects are not covered by the model they are, for instance, not soluble in cyclohexane in the same way as the original. 

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). 

Chemistry is dehned as a study of the elements and their properties. Most of the time chemists are interested not so much in the elements themselves but rather in molecules, which are combinations of elements into discreet units. The organic chemist normally thinks of a molecule by reference to a rather simple model, usually of the ball-and-stick type. Such models are extremely useful for aiding in the visualization of three-dimensional interactions between molecules and between parts of molecules. But they are also a little bit misleading. A real molecule is not static, the way the usual mechanical model is. Rather, it is undergoing rapid motions, both internally and externally. Molecular structure can be defined at different levels, which are useful for different kinds of purposes. As we go past the ball-and-stick model, to the hard sphere model (space-filling model), and then to the soft sphere model (computational chemistry), we obtain an increasingly accurate description of the molecule and its properties. 

Line Electron Pairs Bonded Atoms Electron-Pair Geometry Ball-and-Stick Model Electron-Pair and Bond Angle Molecular Geometry Lewis Diagram Ball-and-Stick Model Space Filling Model Example Actual Bond Angle... 

In a space-filling molecular model, atoms fill the space between each other to more closely represent our best estimates for how a molecule might appear if scaled to visible size. Consider the following ways to represent a molecule of methane, the main component of natural gas ... 

Material models such as coloured plastic molecular scale models (ball-and-stick models, space-filling models),... 

The van der Waals surface (or the hard sphere model, also known as the scale model or the corresponding space-filling model) is the simplest representation of a molecular surface. It can be determined from the van dcr Waals radii of all... 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

FIGURE 1 6 Molecular models of methane (CH4) (a) Framework (tube) models show the bonds connecting the atoms but not the atoms themselves (b) Ball and stick (ball and spoke) models show the atoms as balls and the bonds as rods (c) Space filling models portray overall molecular size the radius of each sphere approximates the van der Waals radius of the atom (d) An electrostatic potential map of methane... 

SpartanBuild software that you can use to build molecular models of various types include tube ball and spoke and space filling This text includes a number of mod eling exercises for you to do but don t limit yourself to them You can learn a lot by sim ply experimenting with SpartanBuild to see what you can make... 

Mesitylene (13 5 trimethylbenzene) is the most stable of the tnmethylbenzene isomers Why2 Which isomer do you think is the least stable" Make a molecular model of each isomer and compare their calculated strain energies with your predictions Do space filling models support your explanation" ... 

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... 

Space filling model (Section 19) A type of molecular model that attempts to represent the volume occupied by the atoms... 

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. 

Space-Filling Models. For most of this century, chemists have tried to answer the size question by using a special set of molecular models known as space-filling or CPK models. The space-filling model of an atom is simply a sphere of fixed radius. A different radius is used for each element, and the radii are chosen to reproduce certain experimental observations, such as the compressibility of a gas, or the spacing between atoms in a crystal. 

Both space-filling and electron density models yield similar molecular volumes, and both show the obvious differences in overall size. Because the electron density surfaces provide no discernible boundaries between atoms (and employ no colors to highlight these boundaries), the surfaces may appear to be less informative than space-filling models in helping to decide to what extent a particular atom is exposed . This weakness raises an important point, however. Electrons are associated with a molecule as a whole and not with individual atoms. The space-filling representation of a molecule in terms of discernible atoms does not reflect reality, but rather is an artifact of the model. The electron density surface is more accurate in that it shows a single electron cloud for the entire molecule. 

The connection between a molecule s electron density surface, an electrostatic potential surface, and the molecule s electrostatic potential map can be illustrated for benzene. The electron density surface defines molecular shape and size. It performs the same function as a conventional space-filling model by indicating how close two benzenes can get in a liquid or crystalline state. 

Another useful way to think about carbon electrophilicity is to compare the properties of the carbonyls lowest-unoccupied molecular orbital (LUMO). This is the orbital into which the nucleophile s pair of electrons will go. Examine each compound s LUMO. Which is most localized on the carbonyl group Most delocalized Next, examine the LUMOs while displaying the compounds as space-filling models. This allows you to judge the extent to which the LUMO is actually accessible to an approaching nucleophile. Which LUMO is most available Least available ... 

Fig. 19. Space filling models of the molecular structure of the Valinomycin-potassium ion complex as originally determined.

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