Chapter 2: Fundamental of Organic Structures

From Secret Recipes to Shared Knowledge

In the early days of chemistry, scientists often kept their discoveries secret – not because they were selfish, but because they wanted to protect their hard work from being stolen or misused. Alchemists, for instance, sometimes used code names or obscure symbols for substances so that only trusted apprentices could reproduce their results.

As chemistry matured into a modern science, attitudes shifted. By the late 1700s, pioneers like Lavoisier and colleagues began to argue that discoveries should be shared openly, so that others could reproduce experiments, test ideas, and build on each other’s work. Today we rely on peer-reviewed publications, conference talks, and databases – and clear communication is essential for all of these.

Why We Need a Systematic Language

Imagine you and a classmate both discover the same new compound, but you each give it a completely different name.  How would others know you are talking about the same molecule?  Or imagine a journal publishes a paper using a name that means something different in another country – these practices would only lead to confusion.

Chemists solved this problem by developing a common language for naming compounds – what we call the systematic chemical nomenclature — based on a defined set of rules and conventions. The goal of this language is to:

• Give each compound one unique name
• Show which atoms are present and how they are connected
• Make it easy to index, search, and discuss chemical information worldwide

This effort led to international collaboration, beginning with the Geneva Rules in 1892 and later the work of the International Union of Pure and Applied Chemistry (IUPAC), which continues to refine and publish the rules we use today.

Your Role as a Future Chemist

In this chapter, you will learn to speak the language of organic chemistry by applying IUPAC’s systematic rules for naming organic molecules. Mastering nomenclature allows you to:

• Communicate unambiguously with other scientists
• Understand chemical literature and databases
• Demonstrate professionalism and precision in your work

Basic Principles: What an Organic Molecule Looks Like

Organic molecules are built mostly from carbon and hydrogen by definition, but other atoms may be present. These other atoms are called heteroatoms . Common heteroatoms  likeare oxygen, nitrogen, sulfur, or and halogens are also commonly present within the structure.

1. Carbon Framework (Skeleton):
   • Forms the “backbone” of the molecules – either a chain or a ring.
   • Can be straight, branched, or cyclic
   • Carbon forms four bonds, allowing for many possible structures
2. Functional Groups:
   • Specific groups of atoms that define the chemical reactivity of the molecule.
   • Examples: -OH (alcohol), -COOH (carboxylic acid), -NH2 (amine).
   • As you notice, most functional groups are made up of heteroatoms. Heteroatoms control the chemical reactivity of molecules through bond polarity and hybridization control the chemical reactivity of molecules.
   • If more than one functional group are present in a molecule, one of the functional groups will be designated as highest-priority functional group and the remaining are considered as substituents (see below)
3. Substituents:
   • Anything attached to the longest carbon framework (branching carbon chains or functional groups other than the highest-priority functional group) is considered a substituent.
4. Stereochemistry:
   • Organic molecules are primarily formed of covalent bonds that are arranged in a specific pattern (configuration) and have a specific direction. The understanding of the 3D arrangement of bonds is called stereochemistry.

Below is an example of a molecule with its IUPAC name. Appreciate the various aspects of the structure of organic molecules discussed above in the example and connect them to the IUPAC name provided.

(Draw and name the molecule (color coded) as in the worksheet) (S,Z)-3-hydroxy-5-methylhept-5-enoic acid