Representing Organic Compounds: Structural Formulas.

Because of the complexity of the structure of many organic compounds, as well as the importance of structure in organic chemistry, the development of shorthand methods for representing the structures of organic compounds has been almost mandatory in order to allow the drawing of structures in a reasonable amount of space and time. There are several different ways of representing organic compounds: we will illustrate each by using tributylcarbinol (Figure 1.8) as an example.







Figure 1.8 The different representations of tributylcarbinol found in organic chemistry are the complete structural formula (a), the connectivity formula (b), the line formula (c), and the condensed structural formula (d). Of these, the line formula has found the most widespread use in modern organic chemistry.

The molecular formula of this compound is C13H28O, and its full structure is shown in Figure 1.8 as (a). This particular representation, in which every atom of the molecule is explicitly drawn, is often referred to as a complete structural formula. Even in a molecule as small as tributylcarbinol, however, it takes considerable space to draw this structure. There are two ways that this structure can be simplified. In the first, one simply omits all hydrogen atoms bound to carbon to give a skeletal structure, formula (b) in Figure 1.8. Thus single simplification, as you can see, makes a dramatic difference in the ease with which one can see the details of the molecular structure: such formulas are very good for showing the connectivity of the atoms in a molecule. It is still, however, possible to simplify the representation of an organic compound even further without compromising its ability to convey useful information about the structure and bonding of the compound. We do this by recognizing that the one element which always occurs in an organic compound is carbon. Because of this one fact, we can omit the symbol for carbon without losing information provided that we remember that there is a carbon atom at every position of the representation where there is no element symbol specified. By omitting the symbols for the carbon atoms in this way, we simplify formula (b) to give formula (c), which is known as a line formula, or, if a ring of atoms is involved, a polygon formula. Today, line and polygon formulas are the formulas most extensively used by organic chemists to represent the structures of organic compounds.

In a line formula, the end of each line, as well as each vertex, is occupied by a carbon atom bearing sufficient hydrogen atoms to complete its octet (unless it is charged). Where less than four lines meet at a vertex, the remainder of the four valencies of the carbon atom are assumed to be occupied by hydrogen atoms. Atoms which are neither carbon nor hydrogen are called heteroatoms, and all heteroatoms are explicitly shown in line formulas. In general, only non-hydrogen and non-carbon atoms are explicitly indicated on a line formula, although hydrogen atoms bonded to heteroatoms are frequently shown, as illustrated in Figure 1.8(c).

An alternative simplification is to write a simple molecular formula for each carbon atom of the molecule individually. This process is particularly well suited to providing formulas in printed formats where it is difficult to incorporate graphics, or where cost of space may be important. For this reason, such formulas are most frequently encountered in printed works because they are very amenable to typesetting. This process gives rise to formula (d) in Figure 1.8, which is usually referred to as a condensed structural formula, or simply a condensed formula. Realistically, the use of condensed structural formulas is limited to open-chain compounds, or to compounds with only one simple ring. In order to generate the condensed structural formula of a compound, one starts by writing each carbon atom individually, as shown in the first example in Figure 1.8(d). If possible, one can then simplify the representation further by gathering any identical groups bonded to the same carbon together in a set of parentheses, as shown in the representation 1.8(e). Still further condensation of the formula can be effected by gathering common repeating groups in each part of the structure together in parentheses and using a subscript to show how many repeats of that particular group there are in that part of the molecule, giving rise to very compact representations such as that in Figure 1.8(f). It is an important skill to be able to take a condensed structural formula and to be able to convert it back to one of the other representations. When faced with this problem, one can remember this one simple rule: condensed formulas are always written from left to right, and they are written one carbon atom at a time.

Early in the nineteenth century, Jöns Jakob Berzelius, the great Swedish chemist, proposed a theory of compound formation which was essentially ionic in nature. While this theory worked well for inorganic compounds, its extension to organic chemistry has not been as successful. Nevertheless, Berzelius did coin the term radical (or radicle, from the Latin radix, a root), a term which was used during the nineteenth century for the part of a compound which remains unchanged during the course of a reaction. One of the first to criticize this idea was the French chemist Jean-Baptiste Dumas, who proposed instead that organic compounds can be viewed as belonging to families. His "type" theory of organic compounds first appeared in 1826, and is remarkable modern in some of its concepts.

The term "radical" still remains part of the organic chemist's vocabulary today, although it is now used in a different sense than originally intended. The original meaning can still be traced, however, to the use of the generic symbol R to designate the unchanging part of an organic compound undergoing a reaction.

The part of the molecule which undergoes a change during the course of a reaction is called the functional group. A functional group is any part of a molecule which is not a carbon-hydrogen or carbon-carbon single bond. In other words, all multiple bonds and all bonds involving heteroatoms (atoms other than carbon or hydrogen) are functional groups. Practically all of the chemistry of organic compounds occurs at functional groups because the electrons in the carbon-carbon and carbon-hydrogen single bonds of the carbon skeleton are seldom directly involved in reactions - they are tightly held between the two nuclei, and they are seldom accessible to external reagents or respond to their influences. In contrast to this, the electrons of the functional groups are usually fairly accessible to an outside reagent. Indeed, it is because of this that organic chemistry is a manageable study at all - because the number of functional groups is limited, the possible reaction types known today is limited, and can be systematized. Several of the most commonly occurring functional groups are given in Table 1.5.

We have just seen that heteroatoms are the only atoms explicitly shown in line formula representations of molecules, and that carbon-hydrogen bonds are not shown at all. Thus, by using line formulas to represent organic molecules, one immediately focuses the reader's attention on the functional groups. It is this effect of drawing the reader's attention to the most important parts of the molecule immediately on seeing the structure that is one of the strengths of the line formula representation of organic compounds. In this book, we will use the generic symbol G to denote a functional group. Thus, the generic symbol for an organic compound will be R-G.

Table 1.5 Some Common Functional Groups

Sample Problem 1.7. What is the molecular formula of each of the following compounds?

Answers: (a) C10H18. (b) C4H8O. (c) C10H14O.

Sample Problem 1.8. Draw the line or polygon representations of each of the following compounds:

(a) (CH2)4. (b) (CH3)3C(CH2)3CH(CH3)2. (c) HOCH2C(CH3)2CH(CH2)2.


Sample Problem 1.9. What is the condensed formula of each of the following compounds?

Answers: (a) CH3CH2CH(CH2CH3)CH(CH3)C(OH)(CH3)CH2C(OH)(CH3)CH2CH3.

(b) (CF2)2CF(CH2OH).