Molecules three-dimensional shapes

Look at the following computer-generated ball-and-stick models of water, ammonia, and methane. Each of these molecules—and every other molecule as well— has a specific three-dimensional shape. Often, particularly for biologically important molecules, three-dimensional shape plays a crucial part in determining the molecule s chemistry. 

Remember that the structural formula does not accurately show the three-dimensional shape of the molecule. Three-dimensional shape is depicted with drawings or models, as shown for ethanol in Figure 1.4. 

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... 

So far we have emphasized structure in terms of electron bookkeeping We now turn our attention to molecular geometry and will see how we can begin to connect the three dimensional shape of a molecule to its Lewis formula Table 1 6 lists some simple com pounds illustrating the geometries that will be seen most often m our study of organic chemistry... 

In this chapter we explored the three dimensional shapes of alkanes and cycloalkanes The most important point to be taken from the chapter is that a molecule adopts the shape that minimizes its total strain The sources of strain m alkanes and cycloalkanes are... 

The three dimensional shapes of many proteins are governed and stabilized by S—S bonds connecting what would ordinarily be remote segments of the molecule We 11 have more to say about these disulfide bridges m Chapter 27... 

When the polypeptide chains of protein molecules bend and fold in order to assume a more compact three-dimensional shape, a tertiary (3°) level of structure is generated (Figure 5.9). It is by virtue of their tertiary structure that proteins adopt a globular shape. A globular conformation gives the lowest surface-to-volume ratio, minimizing interaction of the protein with the surrounding environment. 

The Ball and Wire model is identical to the Wire model, exeept that atom positions are represented by small spheres. This makes it possible to identify all atom locations in all molecules. The Tube model is identical to the Wire model, except that bonds, whether single, double or triple, are represented by single colored tubes. The tubes are useful because they better eonvey the three-dimensional shape of a molecule. The Ball and Spoke model is a variation on the Ibbe model atom positions are represented by colored spheres, making it possible to see all atom locations in all molecules. 

The present review intends to be illustrative rather than comprehensive, and focuses on the results of this study leading to the hypothesis 9 — the three-dimensional shape similarity between interacting groups in reacting molecules is responsible for more specific and precise molecular recognition than would otherwise be achieved — and on the explanation of biological recognition on this basis. 

I The tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape. 

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

Conformation (Section 3.6) The three-dimensional shape of a molecule at any given instant, assuming that rotation around single bonds is frozen. 

A molecule is a three-dimensional array of atoms. In fact, many of a molecule s properties, such as its odor and chemical reactivity, depend on its three-dimensional shape. Although molecular and structural formulas describe the composition of a molecule, they do not represent the molecule s shape. To provide information about shapes, chemists frequently use ball-and-stick models or space-filling models. 

C09-0018. Describe the shape of chloromethane (CICH3). Make a sketch of the molecule that shows its three-dimensional shape. 

Using molecular mechanics calculations to assess the three-dimensional shape of a molecule, various surface properties such as polarity and size can be calculated. The dynamic molecular surface properties can be determined from the (low energy) conformation(s) of the drug molecule obtained by molecular mechanics calculations of conformational preferences. The potential advantage of this method is that the calculated surface character-sitics determine numerous physicochemical properties of the molecules including lipophilicity, the energy of hydration and the hydrogen bond formation capacity [187-... 

A number of different molecular mechanisms can underpin the loss of biological activity of any protein. These include both covalent and non-covalent modification of the protein molecule, as summarized in Table 6.5. Protein denaturation, for example, entails a partial or complete alteration of the protein s three-dimensional shape. This is underlined by the disruption of the intramolecular forces that stabilize a protein s native conformation, namely hydrogen bonding, ionic attractions and hydrophobic interactions (Chapter 2). Covalent modifications of protein structure that can adversely affect its biological activity are summarized below. 

Although structurally-diverse as evidenced above, the insecticidal pyrethroids still conform to a unique, operationally-defined, structure-activity relationship based on the physical characteristics and three-dimensional shape of the entire molecule conforming to those originally evidenced in the natural pyrethrins [13]. From this relationship, it becomes apparent that there is no single molecular aspect or reactive moiety that serves as a true toxophore for the pyrethroids and that their actions at target sites are dependent upon the entire stereospecific structure of these insecticides [1]. 

Creating the Lewis structures of molecules is a method for determining the sequence of bonding within a molecule and its three-dimensional shape. This works best for covalently bonded molecules, but can also work for ionic compounds. For example, this method can be used to explain why the sequence of bonding in water is H-O-H, rather than H-H-O, and why it has a bent structure, rather than linear. 

The standard gel-forming reaction is shown in Figure 8.2. Acrylamide and the cross-linker N, A-methylenebisacrylamide (bis) are mixed in aqueous solution and then copolymerized by means of a vinyl addition reaction initiated by free radicals.1317 Gel formation occurs as acrylamide monomer polymerizes into long chains cross-linked by bis molecules. The resultant interconnected meshwork of fiberlike structures has both solid and liquid components. It can be thought of as a mass of relatively rigid fibers that create a network of open spaces (the pores) all immersed in liquid (the buffer). The liquid in a gel maintains the gel s three-dimensional shape. Without the liquid, the gel would dry to a thin film. At the same time, the gel fibers retain the liquid and prevent it from flowing away. 

The three-dimensional shape of a molecule is particularly important when the molecule contains polar covalent bonds. As you may recall from your previous chemistry course, a polar covalent bond is a covalent bond between two atoms with different electronegativities. 

Predict and sketch the three-dimensional shape of each multiple-bonded molecule. 

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. 

In relating properties of molecules to their structure, three-dimensional shape is frequently of great importance. Three-dimensional shape is a function of many variables the nature and number of atoms composing the molecule and the nature of the chemical bonding pattern— which atoms are connected to which—are obvious factors. However, the situation can be more subtle than that. Even in cases in which the atomic composition of two molecules is the same and in which the chemical bonding pattern is the same, key differences in three-dimensional shape can arise. 

Neurotransmitter/Receptor Binding. At this point, the neurotransmitter chemical is free in the synapse (extracellular fluid) and drifts (diffuses) in all directions. Some of the neurotransmitter molecules float across the synapse and bind to receptors on the surface of the adjacent nerve cell. Each neurotransmitter has its own unique three-dimensional shape and binds with certain receptors but not others. The binding between a neurotransmitter and a receptor is similar to fitting a key into a lock. When the neurotransmitter binds the receptor, the signal has been passed to the neighboring nerve cell. This is the process of neurotransmission. 

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