Structural Formulas of Molecules

In the examples of elements that form inorganic compounds, as discussed in the previous chapter, we usually just give a compound s molecular formula without drawing a picture of 

Molecules of organic compounds, on the other hand, often contain many more atoms than do molecules of inorganic compounds. More importantly, often there are several different ways to connect the atoms together in organic compounds—in chains or rings, for example. Each different way to connect atoms together gives a different structure to the molecule. We call these different structures isomers of a compound. 

Structural formulas show how the atoms are connected together, their relative spatial orientations, and an indication of the distances between atoms and the angles between the bonds that connect atoms. Structure is the key to understanding properties of molecules, especially large molecules. Therefore, it is very common to write structural formulas for organic compounds instead of simple molecular formulas. 

Isomers are compounds that have the same molecular formula, but different structural formulas. In organic chemistry, the properties of substances are determined by the structures of their molecules. 

Because structure is so important, let us begin by establishing some ground rules for how structures are written. First of all, let us look at the kinds of chemical bonds that can exist between atoms. Carbon atoms can form three kinds of bonds, which are the following  

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For most theoretical chemists, debates about the theory of chemical bonding center around the relative merits of the several named theories and their variants. But there is another viewpoint, from which the strongest theory of chemical bonding is not a named numerical theory like any of those discussed so far but a robust graphical calculus that involves drawing and manipulating lines between pairs of atoms in the structural formulas of molecules. The initial idea is that such a line means a pair of valence electrons shared between the atoms at the ends of the hond. This basic idea then undergoes a number of extensions. 

At this point, our concern is only pattern recognition—that is, how to recognize these five functional groups when you see them and how to draw structural formulas of molecules containing them. 

The aforementioned names are systematic names, which are based on actual structural formulas of molecules. In addition, there are common names of organic compounds that do not indicate their structural formulas. Naming organic compounds is a complex topic, and no attempt is made in this chapter to teach it to the reader. Flowever, from the names of compounds given in this chapter and later chapters, some appreciation of the rationale for organic compound names shonld be obtained. 

Strategy Write the condensation reaction that takes place between glycine and serine. To do this, start with the structural formulas of the two amino acids, glycine at the left, serine at the right. In each case, put the NH2 group at the left, the COOH group at the right. Condense out a water molecule what is left is the structural formula of Gly-Ser. 

If all the oxygen containing groups are reduced, n-hexane results. This test helps establish that the glucose molecule has a chain structure. One representation of the structural formula of glucose, C6Hi206, is... 

C03-0010. Draw structural formulas of the following molecules butane, 2-butanol, t-butanol, and t-bromobutane. 

FIGURE 10.1 The structural formula of riboflavin and partial structures of riboflavin compounds. The latter show only those portions of the molecule that differ from riboflavin. 1 — Riboflavin (RF), 2 — flavin mononucleotide or 5 -riboflavin monophosphate (FMN or 5 -FMN), 3 — flavin adenine dinucleotide (FAD). 

FIGURE 10.3 Structural formula of vitamin B[2 and partial structures of vitamin B[2 compounds. The partial structures of vitamin B,2 compounds show only those portions of the molecule that differ from vitamin B[2. 1 — 5 -deoxyadenosylcobalamin, 2 — methylcobal-amin, 3 — hydroxocobalamin, 4 — cyanocobalamin, 5 — benzimidazolyl cyanocobamide, 6 — pseudovitamin B[2, 7 — 5-hydroxybenzimidazolyl cyanocobamide, 8 — p-cresolyl cyanocobamide. 

Structural formulas also provide information on the way the atoms are arranged and bonded to one another within a molecule. The structural formula of substances not only specifies the type of atoms and how many atoms of each type there are in the molecule of a compound it also provides an outline of the structure of the molecule, pinpointing exactly where each atom is located. Each element in a structural formula is represented by its symbol, and the bonds between atoms are indicated by lines connecting the symbols (see Fig. 60). Thus, structural formulas not only provide information on the type and number of atoms in a molecule of a substance but also depict the internal structure of the molecule of the substance. 

The molecules of two organic compounds are sometimes composed of the same type and number of atoms, but arranged in different ways. The molecular formula of each one of such compounds, which are known as isomers (for example, isoleucine and alloisoleucine, shown in Fig. 73), is therefore identical to that of the other only the structural formulas of the two isomers show the differences between their molecules (see Textbox 63). 

The aromatic hydrocarbons are characterized by molecules containing six-membered rings of carbon atoms with each carbon atom attached to a maximum of one hydrogen atom. The simplest member of the series is benzene, ChH6. Using the total bond order rules discussed above, the structural formula of benzene can be written as follows ... 

When the number of carbon atoms in an alcohol molecule is greater than 2, several isomers are possible, depending on the location of the —OH group as well as on the nature of the carbon chain. For example, the structural formulas of four isomeric alcohols with the formula C4HyOH are given in Table 21-6. 

For the depiction of structural formulas of hexofuranoses, a combination of a three-dimensional, Haworth-perspective tetrahydrofuran ring with a Fischer projection of the C-5-C-6 side-chain is commonly used, as exemplified by formulas 3 and 6. With the formal closure of the second ring and formation of a 2,6-dioxabicyclo[3.3.0]octane system, however, the depiction of the C-6-C-3 ring, as in formula 7, also assumes three-dimensional geometry, and this does not correspond to the Fischer projection rule.11 Consequently, structural representations of such bicyclic molecules should be as close as possible to the actual steric situation, as shown by structures 4 and 8. 

The structural formula of a compound not only indicates which atoms are present in the formula unit, but also how they are joined together (represents bonding in the molecule)... 

The structural formula of a compound not only shows the number of each kind of atom in the molecule, but also how the atoms are joined together. The simplest of these structural formulae is the full structural formula, in which all the bonds between the atoms are displayed. For example, the full structural formula of 2,3-dimethylpentan-3-ol is drawn on the left and alongside it are two abbreviated structural formulae. 

State the number of (a) cr bonds and (b) k bonds in a molecule of quinolone. (Hint drawing the full structural formula of quinoline will help.)... 

The variety of methods of naming azo compounds which has been in use for many years may lead to considerable confusion, especially when attempts are made to name structural formulas of highly substituted dye molecules with several azo linkages. Furthermore, in regard to the older dye literature, an intuitive interpretation of an author s intention frequently seems more productive than a detailed analysis of the system of nomenclature which he may be using. An effort is made in this chapter to conform to either the IUPAC or the Chemical Abstracts system [la]. 

Cell membrane lipids are natural surfactants and display most of the properties of synthetic surfactants. The principal difference between these molecules and the surfactants that we discussed above in the chapter is that lipids contain two hydrocarbon tails per molecule. Table 8.5 shows the general structural formula of these cell membrane lipids and the names and formulas for some specific polar head substituents. The alkyl groups in these molecules are usually in the C 6-C24 size range and may be either saturated or unsaturated. 

By considering the structural formula of TNT (5.1) and of nitroglycerine (5.2) the proportion of oxygen in each molecule can be calculated and compared with the amount of oxygen required for complete oxidation of the fuel elements, i.e. hydrogen and carbon. 

In 1861 the Russian chemist A. M. Butlerov, Z. Chem. Pharm. 4, 540 (1861), used the term chemical structure11 for the first time and stated that it is essential to express the structure by a single formula. winch should show how each atom is linked to other atoms in the molecule of the substance. He stated clearly that all properties of a compound are determined by the molecular structure of the substance and suggested that it should be possible to find the correct structural formula of a substance by studying the ways in which it can be synthesized. 

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