Three-dimensional shapes of molecules

Table 1 3 lists the dipole moments of various bond types For H—F H—Cl H—Br and H—I these bond dipoles are really molecular dipole moments A polar molecule has a dipole moment a nonpolar one does not Thus all of the hydrogen halides are polar molecules To be polar a molecule must have polar bonds but can t have a shape that causes all the individual bond dipoles to cancel We will have more to say about this m Section 1 11 after we have developed a feeling for the three dimensional shapes of molecules... 

Line structures also can be modified to represent the three-dimensional shapes of molecules, and the way that this is done will be discussed in detail in Chapter 5. At the onset of your study of organic chemistry, you should write out the formulas rather completely until you are thoroughly familiar with what these abbreviations stand for. 

Although you are probably getting better at seeing the three-dimensional shapes of molecules when viewing two-dimensional representations, it is still worthwhile to construct models to help you understand the material in this chapter. And remember to take advantage of the online computer models that are available for the molecules discussed in this chapter. 

Atomic wave functions with magnetic quantum number m/ = 0 are real functions and their corresponding orbitals can be mapped in the form of well-defined geometrical shapes. Wave functions of electrons with mj 0 are complex functions and do not generate orbitals in real space. But, if by some procedure, these complex functions could be transformed into real orbitals in three-dimensional space, it would in principle be possible to use these spatially directed orbitals to predict the three-dimensional shape of molecules according to the pattern of overlap. The well-known scheme of hybridization by linear combination of atomic orbitals represents such an attempt. 

Shape in chemistry appears on many levels. The shapes of crystals, the shapes of titration curves, the shapes of spectral lines, the shapes of potential energy functions or the multidimensional shapes of potential energy hypersurfaces are some examples. However, few chemists would dispute that the most important shape problem of chemistry is that of the three-dimensional shapes of molecules. The study of molecular shape and molecular shape changes is fundamental to our understanding of chemical properties and reactions. 

The purpose of this book is to acquaint the reader with the topological methods of the description and analysis of shapes, in particular, the three-dimensional shapes of molecules. The topological approach is generally applicable to all aspects of shape in chemistry, hence the title of the book appears justified, although our focus will be on the central shape problem in chemistry on molecular shape. 

Drawing organic molecules ch2 Three-dimensional shape of molecules DIastereoselectIvlty ch34... 

Space-filling model V shows three-dimensional shape of molecule shows most of the space taken by electrons uses false colors to differentiate between elements bonds are not clearly indicated parts of large molecules may be hidden... 

The VSEPR theory predicts the three-dimensional shapes of molecules. It is based on simple electrostatics—electron pairs in a molecule will arrange themselves in such a way as to minimize their mutual repulsion. The steric number determines the geometry of the electron pairs (linear, trigonal pyramidal, tetrahedral, and so forth), whereas the molecular geometry is determined by the arrangement of the nuclei and may be less symmetric than the geometry of the electron pairs. 

In Chapter 3 the reasons why drugs behave as weak adds or weak bases were discussed and strategies were developed to exploit differences in physicochemical properties to separate components of a mixture. In this chapter, the three-dimensional shapes of molecules will be introduced and, in particular, the unusual geometry that arises around a carbon atom with four different substituents attached to it — an asymmetric carbon atom. The study of the three-dimensional shape of molecules is absolutely fundamental to a student s understanding of complex topics such as biochemistry, medicinal chemistry and drug design. 

Figure 2-6 Formulas and models for some molecules. Structural formulas show the order in which atoms are connected but do not represent true molecular shapes. Ball-and-Stick models use balls of different colors to represent atoms and sticks to represent bonds they show the three-dimensional shapes of molecules. Space-fiUing models show the (approximate) relative sizes of atoms and the shapes of molecules.

The writing of Lewis formulas is an electron bookkeeping method that is useful as a first approximation to suggest bonding schemes. It is important to remember that Lewis dot formulas only show the number of valence electrons, the number and kinds of bonds, and the order in which the atoms are connected. They are not intended to show the three-dimensional shapes of molecules and polyatomic ions. We will see in Chapter 8, however, that the three-dimensional geometry of a molecule can be predicted from its Lewis formula. 

VSEPR theory (10) Valence shell electron pair repulsion theory, which predicts the three-dimensional shape of molecules and ions based on the arrangement of electron pairs (nonbonding pairs and bonds) about the central atom. 

The exact three-dimensional shape of molecules is a matter of great importance. 

Predict the three-dimensional shapes of molecules using the VSEPR model. (Section 9.2)... 

As we saw in the previous section, the VSEPR model is a particularly powerful tool in the prediction of the three-dimensional shapes of molecules. However, it does not always predict the correct molecular geometry. In this section, we... 

Even though structural formulas are useful for showing the order of attachment of atoms, they do not show three-dimensional shapes. As chemists try to understand more and more about the relationships between structure and the chemical and physical properties of molecules, it becomes increasingly important to know more about the three-dimensional shapes of molecules. 

A flexible molecule is one that can adopt many different shapes, or conformations. The study of the three-dimensional shapes of molecules is called conformational analysis. This chapter will introduce only the most basic principles of conformational analysis, which we will use to analyze the flexibility of molecules. To simplify our discussion, we will explore compounds that lack a functional group, called alkanes and cycloalkanes. Analysis of these compounds will enable us to understand how molecules achieve flexibility. Specifically, we will explore how alkanes and cycloalkanes change their three-dimensional shape as a result of the rotation of C—C single bonds. 

Performance Models are often used to visualize the three-dimensional shape of molecules. Using gumdrops as atoms and toothpicks to bond them together, construct models of different hydrocarbons. Use large gumdrops for carbon and smaller gum-drops for hydrogen. 

Chapter 10, Properties of Solids and Liquids, introduces electron-dot formulas for molecules and ions with single and multiple bonds as well as resonance structures. Electronegativity leads to a discussion of the polarity of bonds and molecules. Electron-dot formulas and VSEPR theory illustrate covalent bonding and the three-dimensional shapes of molecules and ions. The attractive forces between particles and their impact on states of matter and changes of state are described. Combining Ideas from Chapters 8, 9, and 10 follows as an interchapter problem set. 

More detail about orbital hybridization than provided above is given in Sections 1.9 1.15 of Organic Chemistry. With that greater detail it will be apparent from consideration of orbital hybridization that for three groups of valence electrons the ideal separation is 120° (trigonal planar), and for two groups of valence electrons the ideal separation is 180° (linear). VSEPR theory allows us to come to essentially the same conclusion as by the mathematical hybridization of orbitals, and it will serve us for the moment in predicting the three-dimensional shape of molecules. 

Having established that the molecular shape of methane is tetrahedral, the following question arises How can we represent the three-dimensional shape of molecule on a sheet of paper In the diagram in the margin, we have enclosed a methane molecule in a tetrahedron (red lines). 

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