The Shapes of Molecules

Fitting Together The tiles I n this wall detal frorri the Alhambra i n Granada, Spain interconnect to form a whole. Similarly, biomoleciiles fit together to trigger reactions within organisms. In this chapter, you view a molecule as an object with a specific shape and learn the importance oif shape in reactivity. 

A Lewis structure shows the relative positions of the atoms in the molecule or a polyatomic ion, as well as the placement of all the shared and unshared electron pairs. 

In many molecules or ions one electron pair in a double bond spreads over an adjacent single bond, thereby delocalizing its charge, which stabilizes the system. In such cases, more than one Lewis structure, each called a resonance form, can be drawn, and the species actually exists as a resonance hybrid, a mixture of the resonance forms. 

By assigning to each atom a formal charge based on the electrons belonging to the atom and shared by it, we can select the most important of the various resonance forms. 

A whole molecule may be polar, depending on its shape and the polarities of its bonds. 

The molecular shape of the nitrate ion, N03, is shown here with its bond lengths and bond angles. 

Both the water molecule and the nitrate ion are planar all the atoms lie in the same plane. You could imagine these species lying flat on a tabletop, but most molecules are not planar. The shape of the methane molecule, CH4, is tetrahedral. Connecting the four hydrogen atoms forms a pyramid with four identical sides, thus the name tetrahedral. All H-C-H bond angles are the same, 109.5°, the tetrahedral angle, and all C-H bond lengths are the same. 

Of the two, bond angles and bond lengths, it is the bond angle that better indicates the three-dimensional shape of a species. Three of the most important bond angles are shown in the following three models. Note the name of each shape and the associated bond angle. 

Here is how the VSEPR method is applied to predict the shape of a molecule or polyatomic ion  

Derive the Lewis structure of the species using the rules given previously. If the species displays resonance, choose one resonance form. 

1 Valence Shell Electron Pair Repulsion (VSEPR) Theory 

With lone pairs, minimize the number of crowded 90° interactions, especially with other lone pairs 

Carbon has one 2s and three 2p orbitals that can be used for hybridization (Table 1.4). Combining the 2s and one of the 2p orbitals to get two sp hybrids leaves two 2p orbitals remaining. Because the 2s orbital is lower in energy and closer to the nucleus than a 2p orbital, hybrid orbitals that contain a higher %s character will form bonds that will be shorter, stronger, and lower in energy. 

To determine the hybridization of a carbon atom, just count the atoms it is bonded to An sp carbon bonds to four other atoms, an sp carbon bonds to three, and an sp carbon bonds to only two. Use the Lewis structure for this rather than the line structure because the latter does not show all the hydrogens. 

The requirement that the p orbitals overlap causes a very large barrier to rotation about the double bond, about 63 kcal/mol (264 kJ/mol). Cis (two groups on the same side) and trans (two groups on opposite sides) double-bond isomers do not interconvert at any reasonable temperatures. The trans isomer tends to be slightly more stable than the cis isomer because the groups may bump into one another when they are cis. More alkyl substitution on the double bond (replacing an H on the double bond by an R) makes the alkene slightly more stable. For example, an equilibrium mixture of butenes is found to contain 3% 1-butene, 23% ds-2-butene (R equals CHj above), and 74% /rans-2-butene. 

1 Depicting Moiecuies and ions with Lewis Structures Using the Octet Rule Resonance Formal Charge Exceptions to the Octet Rule 

2 Valence-Shell Electron-Pair Repulsion (VSEPR) Theory and Molecular Shape Electron-Group Arrangements and Molecular Shapes 

Molecular Shape with Two Electron Groups Shapes with Three Electron Groups Shapes with Four Electron Groups Shapes with Five Electron Groups 

Shapes with Six Electron Groups Using VSEPR Theory to Determine Molecular Shape 

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Section 1 10 The shapes of molecules can often be predicted on the basis of valence shell electron pair repulsions A tetrahedral arrangement gives the max imum separation of four electron pairs (left) a trigonal planar arrange ment is best for three electron pairs (center) and a linear arrangement for two electron pairs (right)... 

The geometries obtained from optimizations with semi-empirical calculations describe the shapes of molecules. The calculations have varying degrees of accuracy and take more time than molecular mechanics methods. The accuracy of the results depends on the molecule. 

The bright colors of flowers and the varied hues of autumn leaves have always been a cause for delight, but it was nor until the twentieth century that chemists understood how these colors arise from the presence of organic compounds with common structural features. They discovered how small differences in the structures of the molecules of these compounds can enhance photosynthesis, produce important vitamins, and attract pollinating bees. They now know how the shapes of molecules and the orbitals occupied by their electrons explain the properties of these compounds and even the processes taking place in our eyes that allow us to see them. 

To help us predict the shapes of molecules, we use the generic VSEPR formula ... 

Example the n = 2 shell of Period 2 atoms, valence-shell electron-pair repulsion model (VSEPR model) A model for predicting the shapes of molecules, using the fact that electron pairs repel one another. 

These three frameworks and the framework for glycine in Figure 9 illustrate an important point about Lewis structures. Although Lewis structures show how atoms are connected to one another, a Lewis structure is not intended to show the actual shape of a molecule. Silicon tetrachloride is not flat and square, SO2 is not linear, and the fluorine atoms in CIF3 are not all equivalent. We describe how to use Lewis structures to determine the shapes of molecules later in this chapter. 

VSEPR theory works best when predicting the shapes of molecules composed of a central atom surrounded by bonded atoms and nonbonding electrons. Some of the possible shapes of molecules that contain a central atom are given in Figure 7.11, along with the chemical formulas of molecules that have that shape. 

In Chap. 3 the elementary structure of the atom was introduced. The facts that protons, neutrons, and electrons are present in the atom and that electrons are arranged in shells allowed us to explain isotopes (Chap. 3), the octet rule for main group elements (Chap. 5), ionic and covalent bonding (Chap. 5), and much more. However, we still have not been able to deduce why the transition metal groups and inner transition metal groups arise, why many of the transition metals have ions of different charges, how the shapes of molecules are determined, and much more. In this chapter we introduce a more detailed description of the electronic structure of the atom which begins to answer some of these more difficult questions. 

The shapes of molecules and ions are explained by the valence shell... 

The recent book Conformational Analysis of Molecules in Excited States, by Jacek Waluk, Wiley, New York, 2000, describes the way we can experimentally determine the shapes of molecules in the ground and excited states. It can be a little high brow at... 

Nakatsuji, H. 1974b. Electron-cloud following and preceding and the shapes of molecules. 

The most widely used qualitative model for the explanation of the shapes of molecules is the Valence Shell Electron Pair Repulsion (VSEPR) model of Gillespie and Nyholm (25). The orbital correlation diagrams of Walsh (26) are also used for simple systems for which the qualitative form of the MOs may be deduced from symmetry considerations. Attempts have been made to prove that these two approaches are equivalent (27). But this is impossible since Walsh s Rules refer explicitly to (and only have meaning within) the MO model while the VSEPR method does not refer to (is not confined by) any explicitly-stated model of molecular electronic structure. Thus, any proof that the two approaches are equivalent can only prove, at best, that the two are equivalent at the MO level i.e. that Walsh s Rules are contained in the VSEPR model. Of course, the transformation to localised orbitals of an MO determinant provides a convenient picture of VSEPR rules but the VSEPR method itself depends not on the independent-particle model but on the possibility of separating the total electronic structure of a molecule into more or less autonomous electron pairs which interact as separate entities (28). The localised MO description is merely the simplest such separation the general case is our Eq. (6)... 

The shape of a molecule has quite a bit to do with its reactivity. This is especially true in biochemical processes, where slight changes in shape in three-dimensional space might make a certain molecule inactive or cause an adverse side effect. One way to predict the shape of molecules is the valence-shell electron-pair repulsion (VSEPR) theory. The... 

Besides, the pharmacological actions of many compounds are invariably dependent on the shape of molecules and hence, usually play a very significant role. Therefore, if both cis- and tram-isomers are produced in the course of a particular synthesis it may be absolutely necessary to incorporate in the product profile a specific test for the relative proportions of one to the other. This type of control measure strictly conforms the uniformity of composition in the bulk-drug industry and ensures a check on the batch-to-batch variation. 

If excited molecules can rotate during the excited-state lifetime, the emitted fluorescence is partially (or totally) depolarized (Figure 5.9). The preferred orientation of emitting molecules resulting from photoselection at time zero is indeed gradually affected as a function of time by the rotational Brownian motions. From the extent of fluorescence depolarization, we can obtain information on the molecular motions, which depend on the size and the shape of molecules, and on the fluidity of their microenvironment. 

VSEPR stands for Valence Shell Electron Pair Repulsion and these electron pair repulsions are responsible for the shapes of molecules and polyatomic ions, such as NH+. 

From our discussions of bonding, we have learnt something about the arrangement of bonds around various atoms (see Chapter 2). These concepts are fundamental to our appreciation of the shape of molecules, i.e. stereochemistry. Before we delve into these matters, let us recap a little on the disposition of bonds around carbon. 

Dipole moments have been employed principally in the determination of the shapes of molecules and their, electron distributions. Various experimental procedures for determining dipole moment are discussed in Ref 10, and an extensive tabulation of values is given in Ref 7. The accompanying table lists experimental theoretical values for a variety of expl molecules. The theoretical values were obtd via quantum mechanical procedures... 

D. A. Rees, The Shapes of Molecules Carbohydrate Polymers, Oliver and Boyd, Edinburgh, 1967. 

Drawings showing the effect of van der Waals radii in determining the shapes of molecules are given in Figures 7-13, 7-14, 7-15, and 7-16. 

The concept of the c entralatom is convenient to use in discussing the shapes of molecules. In a simple molecule, one of the atoms usually is "central" to the whole molecule. For example, in CC14 the central atom is C, the one to which all the other atoms are attached. 

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