Organic Molecules

Strong, stable bonds between carbon atoms produce complex molecules containing chains, branches, and rings. The chemistry of these compounds is called organic chemistry. Hydrocarbons are organic compounds composed of only carbon and hydrogen. The alkanes are saturated hydrocarbons—that is, hydrocarbons that contain only single bonds. Alkenes contain one or more carbon-carbon double bonds. Alkynes contain one or more carbon-carbon triple bonds. Aromatic hydrocarbons contain ring structures with delocalized π electron systems. Functional groups related to the carbonyl group include the –CHO group of an aldehyde, the –CO– group of a ketone, the –CO₂H group of a carboxylic acid, and the –CO₂R group of an ester. The carbonyl group, a carbon-oxygen double bond, is the key structure in these classes of organic molecules. All of these compounds contain oxidized carbon atoms relative to the carbon atom of an alcohol group. The addition of nitrogen into an organic framework leads to two families of molecules. Compounds containing a nitrogen atom bonded in a hydrocarbon framework are classified as amines. Compounds that have a nitrogen atom bonded to one side of a carbonyl group are classified as amides. Amines are a basic functional group. Amines and carboxylic acids can combine in a condensation reaction to form amides.

19.1 Functional Groups

Learning Objectives

After completing this section, you will be able to:

Explain why the properties of a given organic compound are largely dependent on the functional group or groups present in the compound.
Identify the functional groups present in each of the following compound types: alkenes, alkynes, arenes, (alkyl and aryl) halides, alcohols, ethers, aldehydes, ketones, esters, carboxylic acids, (carboxylic) acid chlorides, amides, amines, nitriles, nitro compounds, sulfides and sulfoxides.
Identify the functional groups present in an organic compound, given its structure.
Given the structure of an organic compound containing a single functional group, identify which of the compound types listed under Objective 2, above, it belongs to.
Draw the structure of a simple example of each of the compound types listed in Objective 2.

Functional groups are small groups of atoms that exhibit a characteristic reactivity. A particular functional group will almost always display its distinctive chemical behavior when it is present in a compound. Because of their importance in understanding organic chemistry, functional groups have specific names that often carry over in the naming of individual compounds incorporating the groups.

As we progress in our study of organic chemistry, it will become extremely important to be able to quickly recognize the most common functional groups, because they are the key structural elements that define how organic molecules react. For now, we will only worry about drawing and recognizing each functional group, as depicted by Lewis and line structures. Much of the remainder of your study of organic chemistry will be taken up with learning about how the different functional groups tend to behave in organic reactions.

Drawing abbreviated organic structures

Often when drawing organic structures, chemists find it convenient to use the letter 'R' to designate part of a molecule outside of the region of interest. If we just want to refer in general to a functional group without drawing a specific molecule, for example, we can use 'R groups' to focus attention on the group of interest:

Lewis structures for a primary alcohol, a secondary alcohol, an aldehyde, and a ketone.

The 'R' group is a convenient way to abbreviate the structures of large biological molecules, especially when we are interested in something that is occurring specifically at one location on the molecule.

Common Functional Groups

In the following sections, many of the common functional groups found in organic chemistry will be described. Tables of these functional groups can be found at the bottom of the page.

Hydrocarbons

The simplest functional group in organic chemistry (which is often ignored when listing functional groups) is called an alkane, characterized by single bonds between two carbons and between carbon and hydrogen. Some examples of alkanes include methane, CH₄, is the natural gas you may burn in your furnace or on a stove. Octane, C₈H₁₈, is a component of gasoline.

Alkanes

Lewis structure of methane. Lewis structure and bond line drawing of octane.

Alkenes (sometimes called olefins) have carbon-carbon double bonds, and alkynes have carbon-carbon triple bonds. Ethene, the simplest alkene example, is a gas that serves as a cellular signal in fruits to stimulate ripening. (If you want bananas to ripen quickly, put them in a paper bag along with an apple - the apple emits ethene gas, setting off the ripening process in the bananas). Ethyne, commonly called acetylene, is used as a fuel in welding blow torches.

Alkenes and alkynes

Lewis structures of ethene (an alkene) and ethyne (an alkyne).

Alkenes have trigonal planar electron geometry (due to sp² hybrid orbitals at the alkene carbons) while alkynes have linear geometry (due to sp hybrid orbitals at the alkyne carbons). Furthermore, many alkenes can take two geometric forms: cis or trans (or Z and E which will be explained in detail in Chapter 7). The cis and trans forms of a given alkene are different molecules with different physical properties there is a very high energy barrier to rotation about a double bond. In the example below, the difference between cis and trans alkenes is readily apparent.

Lewis structure and bond line drawing of a cis-alkene. The methyl groups are on the same side of the double bond.

Alkanes, alkenes, and alkynes are all classified as hydrocarbons, because they are composed solely of carbon and hydrogen atoms. Alkanes are said to be saturated hydrocarbons, because the carbons are bonded to the maximum possible number of hydrogens - in other words, they are saturated with hydrogen atoms. The double and triple-bonded carbons in alkenes and alkynes have fewer hydrogen atoms bonded to them - they are thus referred to as unsaturated hydrocarbons. Hydrogen can be added to double and triple bonds, in a type of reaction called 'hydrogenation'.

The aromatic group is exemplified by benzene (which used to be a commonly used solvent on the organic lab, but which was shown to be carcinogenic), and naphthalene, a compound with a distinctive 'mothball' smell. Aromatic groups are planar (flat) ring structures, and are widespread in nature.

Aromatics

Functional Groups with Carbon Single Bonds to other Atoms

Halides

When the carbon of an alkane is bonded to one or more halogens, the group is referred to as a alkyl halide or haloalkane. The presence of a halogen atom (F, Cl, Br, or I), is often represented by X due to the similar chemistry of halogens. Chloroform is a useful solvent in the laboratory, and was one of the earlier anesthetic drugs used in surgery. Chlorodifluoromethane was used as a refrigerant and in aerosol sprays until the late twentieth century, but its use was discontinued after it was found to have harmful effects on the ozone layer. Bromoethane is a simple alkyl halide often used in organic synthesis. Alkyl halides groups are quite rare in biomolecules.

Lewis structure of trichloromethane (chloroform), dichlorodifluoromethane (Freon-12), and bromoethane.

Alcohols and Thiols

In the alcohol functional group, a carbon is single-bonded to an OH group (the OH group, by itself, is referred to as a hydroxyl). Except for methanol, all alcohols can be classified as primary, secondary, or tertiary. In a primary alcohol, the carbon bonded to the OH group is also bonded to only one other carbon. In a secondary alcohol and tertiary alcohol, the carbon is bonded to two or three other carbons, respectively. When the hydroxyl group is directly attached to an aromatic ring, the resulting group is called a phenol.

Lewis structures of methanol, a primary alcohol, a secondary alcohol, a tertiary alcohol, and a phenol.

The sulfur analog of an alcohol is called a thiol (the prefix thio, derived from the Greek, refers to sulfur).

Lewis structures of a primary thiol, a secondary thiol, and a tertiary thiol.

Ethers and sulfides

In an ether functional group, a central oxygen is bonded to two carbons. Below are the line and Lewis structures of diethyl ether, a common laboratory solvent and also one of the first medical anaesthesia agents.

Bond line drawing and leis structure of diethyl ether.

In sulfides, the oxygen atom of an ether has been replaced by a sulfur atom.

Bond line drawings of diethylsulfide and tetrahydrothipyran.

Amines

Amines are characterized by nitrogen atoms with single bonds to hydrogen and carbon. Just as there are primary, secondary, and tertiary alcohols, there are primary, secondary, and tertiary amines. Ammonia is a special case with no carbon atoms.

Lewis structures of ammonia, a primary amine, a secondary amine, and a tertiary amine.

One of the most important properties of amines is that they are basic, and are readily protonated to form ammonium cations. In the case where a nitrogen has four bonds to carbon (which is somewhat unusual in biomolecules), it is called a quaternary ammonium ion.

Lewis structures of ammonia, a primary amine, a secondary amine, and a tertiary amine.

Lewis structures of ammonium ion, a primary ammonium ion, and a quaternary ammonium ion.

Note: Do not be confused by how the terms 'primary', 'secondary', and 'tertiary' are applied to alcohols and amines - the definitions are different. In alcohols, what matters is how many other carbons the alcohol carbon is bonded to, while in amines, what matters is how many carbons the nitrogen is bonded to.

On the tertiary alcohol carbon is bonded to three carbons. On the primary amine the nitrogen is bounded to one carbon.

Carbonyl Containing Functional Groups

Aldehydes and Ketones

There are a number of functional groups that contain a carbon-oxygen double bond, which is commonly referred to as a carbonyl. Ketones and aldehydes are two closely related carbonyl-based functional groups that react in very similar ways. In a ketone, the carbon atom of a carbonyl is bonded to two other carbons. In an aldehyde, the carbonyl carbon is bonded on one side to a hydrogen, and on the other side to a carbon. The exception to this definition is formaldehyde, in which the carbonyl carbon has bonds to two hydrogens.

Lewis structure of formaldehyde, an aldehyde, and a ketone.

Carboxylic acids and acid derivatives

If a carbonyl carbon is bonded on one side to a carbon (or hydrogen) and on the other side to a heteroatom (in organic chemistry, this term generally refers to oxygen, nitrogen, sulfur, or one of the halogens), the functional group is considered to be one of the ‘carboxylic acid derivatives’, a designation that describes a grouping of several functional groups. The eponymous member of this grouping is the carboxylic acid functional group, in which the carbonyl is bonded to a hydroxyl (OH) group.

Lewis structures of formic acid and acetic acid (vinegar).

As the name implies, carboxylic acids are acidic, meaning that they are readily deprotonated to form the conjugate base form, called a carboxylate.

Lewis structures of formate and acetate.

In amides, the carbonyl carbon is bonded to a nitrogen. The nitrogen in an amide can be bonded either to hydrogens, to carbons, or to both. Another way of thinking of an amide is that it is a carbonyl bonded to an amine.

Lewis structures of three different amides.

In esters, the carbonyl carbon is bonded to an oxygen which is itself bonded to another carbon. Another way of thinking of an ester is that it is a carbonyl bonded to an alcohol. Thioesters are similar to esters, except a sulfur is in place of the oxygen.

Lewis structures of an ester and a thioester.

In an acid anhydride, there are two carbonyl carbons with an oxygen in between. An acid anhydride is formed from combination of two carboxylic acids with the loss of water (anhydride).

Lewis structure for an anhydride.

In an acyl phosphate, the carbonyl carbon is bonded to the oxygen of a phosphate, and in an acid chloride, the carbonyl carbon is bonded to a chlorine.

Lewis structure of an acyl phosphate and an acid chloride.

Nitriles and Imines

In a nitrile group, a carbon is triple-bonded to a nitrogen. Nitriles are also often referred to as cyano groups.

Lewis structure of a nitrile

Molecules with carbon-nitrogen double bonds are called imines, or Schiff bases.

Lewis structure for two different imines.

Phosphates

Phosphorus is a very important element in biological organic chemistry, and is found as the central atom in the phosphate group. Many biological organic molecules contain phosphate, diphosphate, and triphosphate groups, which are linked to a carbon atom by the phosphate ester functionality.

Lewis structure of inorganic phosphate, an organic phosphate ester, and organic diphosphate ester.

Because phosphates are so abundant in biological organic chemistry, it is convenient to depict them with the abbreviation 'P'. Notice that this 'P' abbreviation includes the oxygen atoms and negative charges associated with the phosphate groups.

Lewis structure of dihydroxyacetone phosphate.

Lewis structure of isopentenyl diphosphate.

Molecules with Multiple Functional Groups

A single compound may contain several different functional groups. The six-carbon sugar molecules glucose and fructose, for example, contain aldehyde and ketone groups, respectively, and both contain five alcohol groups (a compound with several alcohol groups is often referred to as a ‘polyol’).

Lewis structure of glucose. Lewis structure of fructose.

Capsaicin, the compound responsible for the heat in hot peppers, contains phenol, ether, amide, and alkene functional groups.

Bond line drawing of capsaicin.

The male sex hormone testosterone contains ketone, alkene, and secondary alcohol groups, while acetylsalicylic acid (aspirin) contains aromatic, carboxylic acid, and ester groups.

Bond line drawing of testosterone. Bond line drawing of acetylsalicylic acid (aspirin).

While not in any way a complete list, this section has covered most of the important functional groups that we will encounter in biological and laboratory organic chemistry. The table found below provides a summary of all of the groups listed in this section, plus a few more that will be introduced later in the text.

Example 19.1

Identify the functional groups in the following organic compounds. State whether alcohols and amines are primary, secondary, or tertiary.

Answer

a) carboxylate, sulfide, aromatic, two amide groups (one of which is cyclic)

b) tertiary alcohol, thioester

c) carboxylate, ketone

d) ether, primary amine, alkene

Draw one example each (there are many possible correct answers) of compounds fitting the descriptions below, using line structures. Be sure to designate the location of all non-zero formal charges. All atoms should have complete octets (phosphorus may exceed the octet rule).

a) a compound with molecular formula C₆H₁₁NO that includes alkene, secondary amine, and primary alcohol functional groups

b) an ion with molecular formula C₃H₅O₆P ^2- that includes aldehyde, secondary alcohol, and phosphate functional groups.

c) A compound with molecular formula C₆H₉NO that has an amide functional group, and does not have an alkene group.

Functional Group Tables

Exclusively Carbon Functional Groups

Class Name	Specific Example	IUPAC Name	Common Name
alkene	H₂C=CH₂	ethene	ethylene
alkyne	HC≡CH	ethyne	acetylene
arene	C₆H₆	benzene	benzene

Functional Groups with Single Bonds to Heteroatoms

Class Name	Specific Example	IUPAC Name	Common Name
halide	H₃C-I	iodomethane	methyl iodide
alcohol	CH₃CH₂OH	ethanol	ethyl alcohol
ether	CH₃CH₂OCH₂CH₃	diethyl ether	ether
amine	H₃C-NH₂	aminomethane	methylamine
nitro compound	H₃C-NO₂	nitromethane
thiol	H₃C-SH	methanethiol	methyl mercaptan
sulfide	H₃C-S-CH₃	dimethyl sulfide

Functional Groups with Multiple Bonds to Heteroatoms

Class Name	Specific Example	IUPAC Name	Common Name
nitrile	H₃C-CN	ethanenitrile	acetonitrile
aldehyde	H₃CCHO	ethanal	acetaldehyde
ketone	H₃CCOCH₃	propanone	acetone
carboxylic acid	H₃CCO₂H	ethanoic Acid	acetic acid
ester	H₃CCO₂CH₂CH₃	ethyl ethanoate	ethyl acetate
acid halide	H₃CCOCl	ethanoyl chloride	acetyl chloride
amide	H₃CCON(CH₃)₂	N,N-dimethylethanamide	N,N-dimethylacetamide
acid Anhydride	(H₃CCO)₂O	ethanoic anhydride	acetic anhydride

Example 19.2

The following is the molecule for ATP, or the molecule responsible for energy in human cells. Identify the functional groups for ATP.

Answer

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Previous Citation(s)

Kennepohl, D., Farmer, S., Soderberg, T., Morsch, L., & Cunningham, K. (2021). Functional Groups. In Organic Chemistry (McMurray). LibreTexts. https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Organic_Chemistry_(McMurry)/03%3A_Organic_Compounds-_Alkanes_and_Their_Stereochemistry/3.01%3A_Functional_Groups

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