SECTION 5 Molecular Shapes

As outlined in Section III.A, knowledge of the molecular wavefunction implies knowledge of the electron distribution. By setting a threshold value for this function, the molecular boundaries can be established, and the path is open to a definition of molecular shape. A quicker, but quite effective, approach to this entity is taken by assuming that each atom in a molecule contributes an electron sphere, and that the overall shape of a molecular object results from interpenetration of these spheres. The necessary radii can be obtained by working backwards from the results of MO calculations21, or from some kind of empirical fitting22. 

In this section, we construct a model of molecular shape empirically, which means that we base it on rules suggested by experimental observations rather than on more fundamental principles. We proceed in three steps. First, we set up the basic nodel for simple molecules without lone pairs on the central atom. Then, we elude the effects of lone pairs. Finally, we explore some of the consequences of ecular shape. 

It is considered that the calculation described in this section agrees well with the experiments for the liquids that have a strong solvation force such as OMCTS and cyclohexane. It may be more difficult to apply this theory to the liquids that have a molecular shape far from spherical and exhibit weak solvation force. 

Tetrahedral geometry may be the most common shape in chemistry, but several other shapes also occur frequently. This section applies the VSEPR model to four additional electron group geometries and their associated molecular shapes. 

As we describe in Section 94, the bond length of a covalent bond is the nuclear separation distance where the molecule is most stable. The H—H bond length In molecular hydrogen is 74 pm (picometers). At this distance, attractive interactions are maximized relative to repulsive interactions (see Figure 9-2). Having developed ideas about Lewis structures and molecular shapes, we can now examine bond lengths In more detail. 

We cannot generate a tetrahedron by simple overlap of atomic orbitals, because atomic orbitals do not point toward the comers of a tetrahedron. In this section, we present a modification of the localized bond model that accounts for tetrahedral geometry and several other common molecular shapes. 

However, the important new feature of metal alkylidenes (4.51) is metal-carbon pi-bonding. As discussed in Section 2.8, pi bonds between transition metals and main-group elements are of d -p type, much stronger than corresponding p —pn bonds between heavier main-group elements. Compared with simple metal hydrides and alkyls, metal-carbon pi-bonding in metal alkylidenes affects the selection of metal d orbitals available for hybridization and skeletal bond formation, somewhat altering molecular shapes. 

In this section, you studied carbon bonding and the three-dimensional shapes of organic molecules. You learned that you can determine the polarity of a molecule by considering its shape and the polarity of its bonds. In Unit 2, you will learn more about molecular shapes and molecular polarity. In the next section, you will review the most basic type of organic compound hydrocarbons. 

Penicillins are the most widely used of the clinical antibiotics. They contain in their structures an unusual fused ring system in which a four-membered P-lactam ring is fused onto a five-membered thiazolidine. Both rings are heterocyclic, and one of the ring fusion atoms is nitrogen. These heteroatoms do not alter our understanding of molecular shape, since we can consider that they also have an essentially tetrahedral array of bonds or lone pair electrons (see Section 2.6.3). 

Allocate the following species to their appropriate point group i (you may wish to postpone this exercise until you have read the sections about molecular shapes in Chapters 5 and 6) ... 

It is seen that

characteristic behavior suggests that the molecular shape of PBLG in the mixed solvent studied does not differ very much from swollen spheres of randomly coiled polymers at stages where the helical fraction is less than about 0.6. In this connection, it is worth recalling from Chapter C, Section 2.b that the dimensional features of a polypeptide remain close to Gaussian at such stages of helix-coil transition, provided the chain is sufficiently long. 

This section reviews the molecular shape descriptors developed by Amoore, Allinger, Simon et al. and Testa and Purcell. The illustrative examples discussed refer to the odour similarity and cardiotoxic aglycones. One has stressed the methods based on the reference structure because, correctly formulated, these methods seem to offer promising perspectives to model the steric effects in biological systems. Finally, a short discussion of possible connections between steric and other substituent constants (relevant in the context of multicollinearity in QSAR) is included. 

As in previous conferences, the section on catalysis contains the most papers. A general review of the different reactions which can be catalyzed by zeolites is presented by Kh. M. Minachev. H. W. Kouwenhoven discusses the isomerization of paraffins on zeolites. Cracking, isomerization, and electron transfer reactions are discussed in several papers. Correlations between particular activities and physicochemical properties are covered. Selectivities related to crystal size and molecular shapes are also studied. Most of the work is still done on modified Y zeolites, but mor-denite and erionite also receive attention. 

The electron-dot structures described in Sections 7.6 and 7.7 provide a simple way to predict the distribution of valence electrons in a molecule, and the VSEPR model discussed in Section 7.9 provides a simple way to predict molecular shapes. Neither model, however, says anything about the detailed electronic nature of covalent bonds. To describe bonding, a quantum mechanical model called valence bond theory has been developed. 

First, use the VSEPR model described in Section 7.9 to predict the molecular shape of vinyl chloride. Then, assign polarities to the individual bonds according to the differences in electronegativity of the bonded atoms (Figure 7.4), and make a reasonable guess about the overall polarity that would result by summing the individual contributions. 

A variety of polymers containing liquid crystalline crown ethers of the molecular shape discussed in this section is known throughout the literature, most of which originate from Percec s laboratory. 

The compounds presented in this section possess, in most cases, columnar phases as expected from their molecular shape. Aza crown ethers and conventional crowns offer a multitude of possibilities to add functional groups. Possible applications can be seen in the field of sensors or functional channels. Unfortunately, no applications have been reported yet. Addition of polymerizable groups might lead to functional membranes as shown in Scheme 40. 

The dendrimer type with a stilbene scaffold and long-chain end groups mentioned in Section 4.1.5.3 was shown to have a disc-like flattened molecular shape in solution by SAXS and SANS studies performed by Ballauff et al. [51]. 

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