1.5 Molecular models and geometry of molecule
1.5 Molecular models and geometry of molecule
As is clear from the figures in the previous sections, it is not easy to represent the arrangement of atoms that make up molecules onto the two-dimensional plane of a paper even for considerably simple molecules such as methane, ethane and acetylene.
Therefore, since latter half of 19th century, when the importance of stereochemistry was began to be recognized, various molecular models have been devised and some of them have been commercially available to assist chemists. However, previously the molecular models had been used only for research, not for education, because stereochemistry was the limited field of science where only a part of chemists were likely to be interested in. In the 20th century, increased recognition for the stereochemistry especially for chemists studying organic chemistry brought the molecular models into the tool of education.
Figure 1.6 illustrates typical molecular models. Each of them is a model of ethane.
(a) Space filling model (e.g. Stuart model, Courtaulds model) represents spread of electronic cloud. However, they fail to represent atoms inside a molecule clearly. It is not always easy to understand the arrangement of atoms in a complex molecule till one would have some experiences. On the other hand,
(b) skeletal model represents a molecule only with sticks in proportion to the bond length. The utility of this type of model is that it is easier to have a good idea on the bond angles, bond lengths and the shape of whole molecule, which is not so clear in the space filling model.
(c) Stick and ball model can be considered as a variation of (b).
The location of an atom (or rather the location of atomic nucleus) is shown by a ball with several holes. Sticks of appropriate length represent the bonds. The angle of each hole on the ball is fitted to correspond to bond angles, and the length of each sticks are also made proportional to corresponding bond lengths. The utility of this model, which it is often easy to understand chemical structure of a molecule since the balls are colored by elements that they symbolize, can make it to be the most suitable one for education.
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(a) space-filling model |
(b) skeletal model |
(c) ball and stick model |
Figure 1.6 Various molecular models
HGS model is a domestic product, and it is easily available everywhere, and a set for students of modest price is also available. It would be worth obtaining a molecular model, because it is necessary for learning stereochemistry.
HGS model consists in balls (in fact polyhedron) with four holes for sp3hybridized carbon atoms, balls with five holes (two for p orbitals) for sp2hybridized carbon atoms, multipurpose balls with many holes including those for sp hybridization, and plastic rods with various lengths. The balls are color-coded for differentiation. There are balls with many holes to be used to construct complex molecules.
▶go to S1.3 Variety of molecular models
There are two methods to represent multiple bonds by molecular models. In the first method, a multiple bond is represented by means of a bond with a bond length or a bond angle from those of the single bond. Dreiding model is one of the examples. Another method is to represent the multiple bond between atoms directly by some ways. HGS model is of the first method so that it is set balls and sticks suitable to this way, but the model is also ready to the second way. For example, ethylene molecule can be represented by connecting two balls for an sp3 hybridized carbon by two curved bonds (Fig 1.7(a)). As for acetylene, three curved bonds can be applied.
In HGS model, the third method to solute the problem is provided. A double bond can be made up by using balls with five holes and hydrogen atoms and plates for p orbitals (fig 1.7 (b)). Since a molecule will be most stable when two pairs of p orbitals come to overlap most effectively, the most stable structure of ethylene can be achieved by fastening those plates.
(a) the model with bent bonds (b) the model with plates for p orbital
Figure 1.7 Molecular model of ethylene by HGS molecular model
There is some similarity between the problem how to represent a double bond in molecular model and the problem how to represent a C-C single bond. When you build up a molecular model of ethane, geometry of two methyl groups is not fixed, whatever model is chosen. In molecular models, one of the methyl groups can be allowed to rotate while holding the other methyl group. Thus, the shape of whole molecule is changed continuously. However, even if the shape would be changed, bond angles and bond lengths are not changed. What is changing is the distance between hydrogen atoms of those two methyl groups.
Suppose you choose one of the hydrogen atoms of each methyl groups and name these HA and HB, respectively. It is clear that the distance between HA and HB is changing by the rotation of the methyl groups, and this can be described by the change of dihedral angle defined by four atoms HA-C-C-HB (Fig.1.8 a, b).
Figure 1.8 The shape of ethane and the dihedral angle
Then, does the change that is taken place in molecular models correspond to the actual phenomenon? Or is it only the result of imperfection with models? It have been widely recognized that such a free rotation around a carboncarbon single bond is possible more than a handled years ago. By the middle of 20th century, further understanding has been developed and such a rotation is not completely free but restricted to some degree restricted rotation.
How are structure, character and reactivity of a molecule influenced by the rotation? This is also an interesting issue with stereochemistry.