7.1: Representing Organic Molecules
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Depending on the size of molecules, how much detail we need to show, and the resources available (paper and pencil vs. Microsoft Word vs. a program designed to draw chemical structures), we use different methods of representing organic molecules on paper. This section shows some of the formulas that will be used in this chapter.
Molecular Formulas
You are already familiar with molecular formulas which indicate the number of each atom, e.g. CH4, CH3O, etc. This is the simplest way to represent a molecule. Unfortunately, molecular formulas cannot uniquely identify big organic molecules because the only information provided is the number of atoms for each element. Organic molecules can have many atoms of just a few different elements with different bonding patterns or in chains of various sizes. In order to distinguish molecules that have the same number of atoms bonded in a different way, more detailed formulas are needed to uniquely identify a molecule.
Structural Formulas
Structural formulas can uniquely identify an organic molecule because they show all the atoms and how they are bonded to one another. They are the same as the Lewis structures you have already learned, except that lone pairs are omitted. You are expected to be able to tell where the lone pairs are because we keep working with the same elements over and over again in organic chemistry. Hydrogen and carbon never get any lone pairs. Nitrogen usually has one lone pair and oxygen usually has two lone pairs.
Condensed Structural Formulas
Some organic structures are quite large, and it can be time consuming to draw all of the atoms and bonds. In addition, chains branching off the main chain can get in the way of one another in a two-dimensional drawing that represents a three-dimensional structure. Condensed structural formulas are like a hybrid between molecular formulas and structural formulas. They group hydrogen atoms with carbon atoms because you always know how they will be bonded (hydrogens can only form single bonds). Therefore, you can concentrate on how the carbon atoms and any other atoms (oxygen, nitrogen, etc.) are bonded.
Example: Propane, C3H8, would be written as CH3CH2CH3
Single bonds between carbon atoms may or may not be shown, so an equivalent condensed structural formula for propane would be CH3-CH2-CH3. Any double or triple bonds must be shown explicitly as in the molecules propene, CH2=CHCH3, and acetylene, HC≡CH.
Branches are shown coming off the main chain, either above or below. The molecule 2-methylbutane can be represented by the following condensed structural formula:
In large organic molecules with repeating structures, such as polymers which are discussed at the end of this chapter, identical groups may be written together. For example, n-hexane, CH3CH2CH2CH2CH2CH3, can be written as CH3(CH2)4CH3 where the four CH2 groups in a row are grouped together in parentheses with a subscript telling how many there are.
Skeletal Formulas
Skeletal formulas omit the hydrogens that are bonded to carbon. This means less writing, but also means that the reader is expected to know that carbon always forms four bonds. In addition, the carbon atoms are frequently represented as points at the ends of lines. Any other atoms present, like oxygen and nitrogen, must be shown explicitly (the hydrogens attached to these atoms should be shown). The following is a skeletal structure for 1-butane or CH3-CH2-CH2-CH3:
The four carbon atoms are represented by the ends of the three lines: the terminus on the left, the two vertices in the middle, and the terminus on the right. Because the carbon on the left is shown bonded to one thing, the neighboring carbon, the reader knows that there must be three hydrogen atoms singly bonded to the carbon. Likewise, because the second carbon atom is at the corner between two lines, it is known that it has two single bonds to carbon atoms. Therefore it must also have two hydrogen atoms.
Any other atoms present, or any double and triple bonds, must be shown explicitly as in the examples below.
From left to right these skeletal structures represent: CH3-CH2-O-CH3, CH3-CH2-CH2-NH2, and CH3-CH=CH2. Double check that you understand these drawings by counting the number of carbon atoms. Notice that when another atom is present, such as the oxygen atom in the first example and the nitrogen atom in the second example, the end of the line does not indicate a carbon atom. That is, there are only three carbon atoms in each of the examples above. Also double check that you can count the hydrogen atoms when they are not included in the drawing.
Remember that double bonds must be shown in skeletal structures. Six-membered rings of carbon are common in organic chemistry. The structures below represent cyclohexane, which contains all single bonds, and benzene which has alternating double and single bonds.
