1.1 Basic Principles of Systematic Naming
1.2.1 Anatomy of an Organic Molecule
Organic molecules are built mostly from carbon and hydrogen by definition but heteroatoms like oxygen, nitrogen, sulfur, or halogens are also commonly present within molecules. The method of systematic nomenclature of organic molecules is mainly based on the method of substitutive nomenclature. The molecule is treated as a combination of a hydrocarbon parent compound where hydrogen atoms along the parent skeleton can be substituted with various carbon and heteroatomic groups. The systematic name provides information on–
- Carbon Framework (Skeleton): This is the “backbone” of the molecule and can be either a linear chain or a ring. The property of carbon called catenation (hyperlinks to chapter 1) allows for various linear, branched and ring structures. You will learn rules to identify the most prominent carbon framework as the “parent compound”
- Functional groups: Specific combinations of atoms that impart specific chemical characteristics (function) to the organic molecule are called functional groups. For example, the carboxylic acid (-COOH) group in vinegar imparts it the characteristic sour taste and acidity.
- Substituents: The ‘parent compound’ can be decorated with carbon structures branching off at different locations. These branches are called substituents. Many organic molecules can have more than one functional group in their structure. While they maintain their ability to impart specific chemical properties to the molecules, for naming purposes, one ‘priority’ functional group is added as a suffix of the ‘parent’ name, and the remaining functional groups are also characterized as substituent functional groups.
- Stereochemistry: The sp3 and sp2 hybridization (hyperlinks to chapter 1) of carbon provide spatial distinction to the atoms and groups attached. While it may sound surprising now, switching the spatial orientation of a bond on carbon can change physical and chemical properties of the molecule. The understanding of the 3D-arrangement of bonds is called stereochemistry and incorporated in the systematic name when the arrangement is asymmetric (hyperlinks to chapter 3?).
Below is an example of a molecule with its IUPAC name. Notice the various aspects of the structure of organic molecules discussed above in the example and connect them to the IUPAC name provided.
(S,Z)-3-hydroxy-5-methylhept-5-enoic acid
An IUPAC name is like a code, where each part provides information about the structure of the molecule. Let’s break down the above example.
| Part | Interpretation |
|---|---|
| (S, Z) | Stereochemistry: R/S denote two possible 3D-arrangements around an asymmetric sp3 carbon, while E/Z denote the two possible arrangements across a double bond. |
| 3-hydroxy | Prefix: Provides location and name of a substituent functional group at position-3. |
| 5-methyl | Prefix: Provides location and name of a substituent carbon group (branch) at position-5. |
| hept | Parent/Root compound: The ‘parent’ carbon skeleton is made of 7-carbons indicated in the name hept = 7. |
| 5-en | Infix: When double or triple bonds are present along with a high priority functional group they are added between the ‘root’ and ‘suffix’ along with their location number. |
| oic acid | Suffix: The highest priority functional group in this molecule is carboxylic acid represented by the ‘oic acid’ suffix. |
1.2.2 Families of Organic Molecules and Functional Groups
Organic molecules can be grouped into families based on their functional group (or the most prominent functional group).
a. Hydrocarbons – The Simplest Family.
| Family | General Structure | Example |
|---|---|---|
| Alkane | R-H (Single bonds only) | CH3–CH2–CH2–CH3 |
| Alkene | R–CH=CH–R | CH3–CH2–CH2–CH=CH–CH3 |
| Alkyne | R–C≡C–R | CH3–C≡C–CH2–CH3 |
| Arene | Ring structures with alternating π-bonds | C6H6 |
Hydrocarbons, as the name suggests, are molecules made of only carbon and hydrogen atoms. There are no heteroatoms present in the structure. They form the foundation for most organic structures and can be divided into four families – alkanes, alkenes, alkynes, and arenes. Alkanes are considered saturated hydrocarbons because every valency of carbon is satisfied by bonding to an individual bonding partner-atom; there are no multiple bonds. Alkenes and Alkynes do not have sufficient atoms to saturate the valency of every carbon, and thus, multiple bonding between carbons can occur in one or more locations within the molecule. Arenes have a special kind of unsaturation that leads to the property of aromaticity and will be discussed later.
*Note: Other families will still have the underlying hydrocarbon structures, but their physical properties and/ or chemical reactivities will be dominated by the functional group/s present along the hydrocarbon structure.
Concept of the R-group:
In the table above, and throughout this book, you will often notice the alphabet R attached to various structures. What does the “R’ represent?
R (or R’, R”, etc.) stands for any generic carbon structure – linear or branched chain, or cyclic carbon structures. When an organic chemist wants to draw attention to a specific part of the molecule the remainder of the molecule can be concisely described by the R-group. For example, in the functional group tables, the intention is to draw your attention to the atoms that form the functional group. Hence, the remaining part of the molecules is designated as an ‘R-group’. When you consider the examples in the third column, you can appreciate that the R-group can be as small as a methyl group or a more complex structure.
b. Functional Groups Containing Oxygen as the Heteroatom.
| Family | General Structure | Example |
|---|---|---|
| Alcohol | R-OH | CH3–CH2–CH2–OH |
| Ether | R–O–R’ | CH3–CH2–CH2–O–CH3 |
| Aldehyde | R–CHO | CH3–CH2–CH2–(C=O)-H |
| Ketone | R–CO–R’ | CH3–(C=O)–CH2–CH3 |
| Carboxylic acid | R–COOH | CH3–CH2–(C=O)-OH |
| Ester | R–COO–R’ | CH3–CH2–(C=O)-O-CH3 |
| Anhydride | (RCO)₂O | CH3–(C=O)-O-(C=O)-CH3 |
c. Functional Groups Containing Nitrogen as the Heteroatom
| Family | General Structure | Example |
|---|---|---|
| Amine | R–NH2, R–NHR’, R–NR’R” | CH3–CH2–NH–CH3 |
| Imine | R–CH=N–R | CH3–CH2–CH2–CH=N–CH3 |
| Nitrile | R–C≡N | N≡C–CH2–CH3 |
d. Functional Groups Containing Halogen as the Heteroatom.
| Family | General Structure | Example |
|---|---|---|
| Alkyl halides | R–X, (X = F, Cl, Br, I) | CH3–CH2–Cl |
| Aryl halides | Ar–X (X = F, Cl, Br, I) | C6H5–F |
*The Ar-group represents an arene ring like how the R-group represents an alkyl group.
e. Functional Groups Containing Sulfur as the Heteroatom.
| Family | General Structure | Example |
|---|---|---|
| Thiol | R–SH (similar to an alcohol but sulfur instead of oxygen) | CH3–CH2–SH |
| Sulfide | R–S–R’ (similar to an ether but sulfur instead of oxygen; also called thioether) | CH3–CH2–CH2–S–CH3 |
| Disulfide | R–S–S –R’ | CH3–S–S–CH2–CH3 |
| Thioester | R–COS–R’(similar to an ester but sulfur replaces the single-bonded oxygen) |
Media Attributions
- (S,Z)-3-hydroxy-5-methylhept-5-enoic acid
