Organic Chemistry

1. Organic Chemistry Explores Molecular Structure and Reactions

Organic chemistry is something more. It literally creates itself as it grows.

The Science of Molecules. Organic chemistry is the study of carbon-containing compounds, their structures, properties, reactions, and synthesis. It bridges physics, mathematics, and biology to understand the molecular world, from the simplest hydrocarbons to the complex molecules of life.

From Life's Tentative Beginnings to Confident Basis. Beginning as an attempt to understand the chemistry of life, organic chemistry has evolved into a field that creates new materials, dyes, perfumes, and drugs. It is a science that both studies and creates molecules, constantly expanding its understanding and capabilities.

Organic Chemistry is a Creative Endeavor. Organic chemistry is not just about understanding existing molecules but also about creating new ones. This creative aspect has led to the development of plastics, dyes, pharmaceuticals, and other essential materials, improving the quality of life for millions.

2. Drawing Conventions Simplify Molecular Representation

Organic chemistry is a visual, three-dimensional subject and the way you draw molecules shows how you think about them.

Visual Language. Organic chemistry relies heavily on structural diagrams to represent molecules. The way these diagrams are drawn reflects how chemists think about and understand the three-dimensional nature of molecules.

Guidelines for Clarity:

• Chains of atoms should be drawn as zig-zags to represent realistic bond angles.
• Hydrogen atoms attached to carbon atoms are usually omitted for clarity.
• Carbon atoms themselves are often omitted, with line junctions representing carbon atoms.

Balance of Realism and Economy. The goal is to create diagrams that are both realistic and economical, conveying essential information without unnecessary clutter. This allows chemists to communicate effectively and efficiently about complex molecular structures.

3. Spectroscopy Unveils Molecular Architecture

For this reason we first reveal to students the facts which spectroscopy tells us (Chapter 3) before trying to explain them (Chapter 4) and then use them to deduce mechanisms (Chapter 5).

Spectroscopy as a Tool. Spectroscopy is a set of experimental techniques that use the interaction of molecules with electromagnetic radiation to determine their structure. Different types of spectroscopy provide complementary information, from bond lengths and angles to the types of functional groups present.

Key Spectroscopic Methods:

• Mass spectrometry: Determines the molecular weight and atomic composition of a compound.
• Nuclear magnetic resonance (NMR): Reveals the symmetry, branching, and connectivity of the carbon skeleton.
• Infrared (IR) spectroscopy: Identifies the functional groups present in the molecule.

Experiment Before Explanation. By first revealing the facts that spectroscopy tells us, we can then use these facts to deduce mechanisms and understand the structure of molecules. This approach emphasizes the importance of experimental evidence in organic chemistry.

4. Molecular Orbitals Dictate Molecular Shape and Reactivity

The best way to find out how something works is to take it apart and put it back together again, so we started with the tools for expressing chemical ideas: structural diagrams and curly arrows.

Electrons as Glue. Molecules are held together by the attraction between positively charged nuclei and negatively charged electrons. Electrons occupy specific energy levels and spatial arrangements called molecular orbitals.

Molecular Orbitals from Atomic Orbitals:

• Atomic orbitals combine to form bonding and antibonding molecular orbitals.
• Bonding orbitals are lower in energy and promote stability, while antibonding orbitals are higher in energy and destabilize the molecule.
• The shape and energy of molecular orbitals dictate the three-dimensional structure and reactivity of molecules.

Hybridization and Molecular Shape. The hybridization of atomic orbitals (sp, sp2, sp3) determines the geometry of molecules. For example, sp3 hybridization leads to tetrahedral structures, while sp2 hybridization leads to trigonal planar structures.

5. Reaction Mechanisms Describe Electron Flow

The dynamic process by which this happens is called mechanism and is the grammar of organic chemistry—the way that one molecule can change into another.

Chemical Transformations. Chemical reactions involve the transformation of molecules into other molecules. The dynamic process by which this happens is called a mechanism.

Nucleophiles and Electrophiles:

• Nucleophiles are electron-rich species that donate electrons to form new bonds.
• Electrophiles are electron-deficient species that accept electrons to form new bonds.

Curly Arrows as a Language. Curly arrows are used to represent the movement of electrons in reaction mechanisms. They show the flow of electrons from nucleophiles to electrophiles, illustrating how bonds are broken and formed during a reaction.

6. Carbonyl Chemistry: A Central Theme

We shall use a mechanistic classification rather than a structural classification and explain one type of reaction rather than one type of compound in each chapter.

The Carbonyl Group's Importance. The carbonyl group (C=O) is one of the most important functional groups in organic chemistry. It is present in aldehydes, ketones, carboxylic acids, esters, amides, and many other compounds.

Mechanistic Classification. Organic chemistry can be organized according to reaction mechanisms rather than structural classifications. This approach allows us to understand the underlying principles that govern the behavior of different types of compounds.

Nucleophilic Addition to Carbonyls. A key reaction of carbonyl compounds is nucleophilic addition, in which a nucleophile attacks the carbon atom of the carbonyl group, forming a new bond and breaking the π bond. This reaction is fundamental to many important transformations in organic chemistry.

7. Controlling Reactions: Selectivity and Protecting Groups

We will then spend two chapters revisiting some of the reactions you have met before in two chapters on selectivity: how to get the reaction you want to happen and avoid the reaction you don’t.

Selectivity in Organic Reactions. Organic molecules often contain multiple functional groups that can potentially react with a given reagent. Selectivity refers to the ability to control which functional group reacts and how it reacts.

Types of Selectivity:

• Chemoselectivity: Choosing which functional group reacts.
• Regioselectivity: Choosing where a functional group reacts.
• Stereoselectivity: Choosing how a functional group reacts (stereochemistry of the products).

Protecting Groups. Protecting groups are temporary modifications that render a functional group unreactive, allowing other reactions to be carried out selectively. After the desired transformation, the protecting group can be removed to restore the original functional group.

8. Pericyclic Reactions: A Symphony of Orbital Symmetry

All science must be underpinned by evidence, and support for organic chemistry’s claims is provided by spectroscopy.

Cycloadditions. Cycloadditions are a type of pericyclic reaction in which two or more unsaturated molecules combine to form a cyclic product. These reactions involve the concerted reorganization of electrons in a ring, without any charged intermediates.

Woodward-Hoffmann Rules:

• Thermal pericyclic reactions with (4n + 2) π electrons proceed with suprafacial geometry.
• Thermal pericyclic reactions with (4n) π electrons proceed with antarafacial geometry.

Diels-Alder Reaction. The Diels-Alder reaction is a [4 + 2] cycloaddition between a conjugated diene and a dienophile. It is a powerful method for forming six-membered rings with excellent control over stereochemistry.

9. Rearrangements and Fragmentations: Molecular Transformations

We aim to avoid dogma and promote the healthy weighing up of evidence, and on occasion we are content to leave readers to draw their own conclusions.

Rearrangements. Rearrangements are reactions in which the carbon skeleton of a molecule changes. These reactions often involve the migration of a group from one atom to another within the molecule.

Fragmentations. Fragmentations are reactions in which a molecule breaks apart into two or more smaller fragments. These reactions often involve the cleavage of carbon-carbon bonds.

Neighbouring Group Participation. Neighbouring groups can accelerate substitution reactions by stabilizing the transition state. This can lead to rearrangements or retention of configuration.

10. Organometallic Chemistry: Expanding Synthetic Horizons

Transition metals extend the range of organic reactions.

Transition Metals as Catalysts. Transition metals play a crucial role in many organic reactions, acting as catalysts to facilitate a wide range of transformations. They can coordinate with organic molecules, activate bonds, and promote new bond formations.

The 18-Electron Rule. The 18-electron rule is a guideline for predicting the stability of transition metal complexes. It states that stable complexes tend to have 18 valence electrons around the metal center.

Palladium Catalysis. Palladium is one of the most widely used metals in homogeneous catalysis. It is involved in a variety of reactions, including the Heck reaction, cross-coupling reactions, and allylic alkylations.

11. Asymmetric Synthesis: Nature's Mirror and the Chiral Pool

Nature is asymmetric.

Chirality in Nature. Many biological molecules are chiral, meaning they exist as non-superimposable mirror images (enantiomers). Nature often uses only one enantiomer of a chiral molecule, leading to specific biological effects.

The Chiral Pool. The chiral pool refers to the collection of readily available, enantiomerically pure natural products that can be used as starting materials for asymmetric synthesis.

Asymmetric Catalysis. Asymmetric catalysis involves the use of chiral catalysts to promote the formation of a single enantiomer of a chiral product. This is a powerful method for creating complex molecules with high stereocontrol.

12. Organic Chemistry's Role in Life and the Future

Science advances through interaction between disciplines.

Primary Metabolism. Primary metabolism encompasses the essential biochemical processes that sustain life, including the synthesis and degradation of nucleic acids, proteins, sugars, and lipids.

Natural Products. Natural products are organic compounds produced by living organisms. They often have complex structures and diverse biological activities, making them valuable sources of new drugs and materials.

Interdisciplinary Science. Organic chemistry is increasingly interdisciplinary, with strong connections to biology, medicine, materials science, and other fields. The future of organic chemistry lies in its ability to address complex challenges in these areas, such as developing new treatments for diseases and creating sustainable materials.

Last updated: April 21, 2025