An Expert Guide to Organic Chemistry for the IMAT

1.1 Carbon: Bonding and Hybridization

Organic chemistry is the study of carbon compounds. Carbon's unique ability to form four stable, covalent bonds (tetravalency) allows for the immense structural diversity of organic molecules. This is explained by the concept of orbital hybridization.

Hybridization (Alkanes)

In hybridization, one 2s and three 2p orbitals mix to form four identical hybrid orbitals. These arrange in a tetrahedral geometry with bond angles of 109.5°. This configuration maximizes the distance between electron pairs, minimizing repulsion. It is characteristic of alkanes, which contain only single sigma () bonds. A bond is formed by the direct, head-on overlap of orbitals, resulting in a strong bond with electron density concentrated along the internuclear axis.

📸 Source/Description: Figure 1.1: sp³ hybridization in carbon leading to the tetrahedral geometry of methane.

Hybridization (Alkenes)

In hybridization, one 2s and two 2p orbitals mix to form three hybrid orbitals, leaving one p orbital unhybridized. The three orbitals adopt a trigonal planar geometry with 120° angles. This orbital arrangement allows for the formation of a double bond, which consists of one bond (from the head-on overlap of orbitals) and one pi () bond. The bond is formed by the sideways overlap of the unhybridized p orbitals above and below the plane of the molecule. This bond is weaker than the bond and is a region of high electron density, making alkenes reactive towards electron-seeking reagents (electrophiles).

Hybridization (Alkynes) - A Deeper Look

In hybridization, one 2s orbital mixes with just one 2p orbital. This creates two equivalent hybrid orbitals arranged in a linear geometry (180°), while two p orbitals remain unhybridized. This orbital arrangement has profound consequences:

• High s-character: Each orbital is 50% s-character and 50% p-character. Since s-orbitals are closer to the nucleus than p-orbitals, the high s-character means that electrons in orbitals are held more tightly to the nucleus. This results in shorter and stronger bonds.
• Increased Electronegativity: This tight hold on electrons makes an -hybridized carbon more electronegative than or carbons.
• Acidity of Terminal Alkynes: The increased electronegativity of the carbon polarizes the C-H bond in a terminal alkyne (e.g., in ethyne, ). This makes the hydrogen atom significantly acidic and allows it to be removed by a strong base (like ).
• Triple Bond Formation: The triple bond consists of one strong bond from the head-on overlap of two orbitals, and two weaker bonds from the side-by-side overlap of the two pairs of unhybridized p-orbitals, which are perpendicular to each other. This creates a cylindrical region of electron density around the internuclear axis.

📸 Source/Description: Figure 1.2: Bonding in ethyne (C₂H₂). The linear sigma framework and two perpendicular pi bonds form a cylinder of electron density.

1.2 Resonance: Delocalized Electrons

Sometimes, a single Lewis structure is insufficient to describe the bonding in a molecule. Resonance occurs when electrons (typically in bonds or lone pairs) can be moved to generate multiple valid Lewis structures, known as resonance contributors. The actual molecule is a "resonance hybrid" of these contributors, and is more stable than any single contributor would suggest. This increased stability is called resonance energy.

Key rules for resonance: 1) Only electrons move, not atoms. 2) The total number of electrons and the net charge must remain constant. 3) Structures with more bonds and less formal charge separation are more significant contributors.

📸 Source/Description: Figure 1.3: The two main resonance contributors of benzene. The actual structure is a hybrid with delocalized electrons across all six carbons, often depicted as a circle inside the hexagon.

1.3 Isomerism: Same Formula, Different Structures

Isomers are different compounds that share the same molecular formula but have different arrangements of atoms. This concept is fundamental to understanding the diversity of organic compounds. For the IMAT, it is crucial to distinguish between the major classes of isomers.

📸 Source/Description: Figure 1.4: A flowchart showing the main classifications of isomers.

Structural (Constitutional) Isomers

These isomers have different bonding connectivity, meaning the atoms are linked in a different order. They have different physical and chemical properties.

• Chain Isomers: Differ in the arrangement of the carbon skeleton. E.g., Butane and 2-methylpropane (isobutane), both .
• Positional Isomers: Differ in the position of a functional group on the carbon chain. E.g., Propan-1-ol and propan-2-ol, both .
• Functional Group Isomers: Have different functional groups. E.g., Ethanol () and dimethyl ether (), both .

Stereoisomers

These isomers have the same connectivity but differ in the 3D spatial orientation of their atoms.

Geometric (Cis/Trans and E/Z) Isomers

This type arises from restricted rotation around a bond, most commonly a C=C double bond.

Cis/Trans: Used when each carbon of the double bond is attached to a hydrogen and another group. 'Cis' means the non-hydrogen groups are on the same side; 'trans' means they are on opposite sides.

E/Z Notation: A more general system used when the C=C bond has three or four different substituents. Priorities are assigned to the groups on each carbon based on atomic number (Cahn-Ingold-Prelog rules). (Z) - from German *zusammen* (together): highest priority groups are on the same side. (E) - from German *entgegen* (opposite): highest priority groups are on opposite sides.

📸 Source/Description: Figure 1.5: Geometric isomers of 2-butene, showing cis (same side) and trans (opposite sides) arrangements. Both are examples of (Z) and (E) isomers, respectively.

Optical Isomers (Enantiomers & Diastereomers)

These isomers arise from chirality, the property of "handedness". A molecule is chiral if it is non-superimposable on its mirror image.

• Chiral Center: A carbon atom bonded to four different groups. This is the most common source of chirality.
• Enantiomers: A pair of molecules that are non-superimposable mirror images of each other. They have identical physical properties (boiling point, solubility) except for their interaction with plane-polarized light (they rotate it in equal but opposite directions) and their interaction with other chiral molecules. A 50:50 mixture of two enantiomers is called a racemic mixture and is optically inactive.
• Diastereomers: Stereoisomers that are NOT mirror images of each other. This occurs in molecules with two or more chiral centers. Diastereomers have different physical and chemical properties.
• Meso Compounds: An achiral compound that has chiral centers. It is superimposable on its mirror image due to an internal plane of symmetry.

📸 Source/Description: Figure 1.6: A general example of enantiomers, showcasing the mirror-image relationship of two chiral molecules.

2.1 Systematic IUPAC Nomenclature

The International Union of Pure and Applied Chemistry (IUPAC) system provides a logical, unambiguous name for every organic compound. Mastering this "language" allows you to deduce a structure from a name and vice-versa, a critical skill for the IMAT.

Core IUPAC Procedure:

1. Identify the Principal Functional Group: This determines the molecule's class and the suffix of the name (e.g., '-ol' for alcohols, '-oic acid' for carboxylic acids). A priority order must be known (see table below).
2. Find the Parent Chain: Select the longest continuous carbon chain that contains the principal functional group. If there are double or triple bonds, the parent chain must contain them. This defines the root name (e.g., 'hexane'). For cyclic compounds, the ring is usually the parent structure.
3. Number the Parent Chain: Number the carbons in the chain so that the principal functional group has the lowest possible number. If there is no functional group with a suffix, number to give multiple bonds the lowest locants. If there are only substituents, number to give them the lowest locants at the first point of difference.
4. Name and Number Substituents: Identify all groups attached to the parent chain. Name them (e.g., 'methyl', 'ethyl', 'bromo', 'hydroxy', 'oxo') and indicate their position with a number.
5. Assemble the Full Name: List substituents alphabetically (ignoring prefixes like 'di-', 'tri-', 'sec-', 'tert-'). Use prefixes like 'di-', 'tri-', 'tetra-' for multiple identical groups. Combine all parts: (Positions)-(Prefixes)-(Parent Chain Root)-(Position of multiple bonds)-(Suffix). For example, 3-methylhex-1-ene.

Example: Naming a Complex Molecule

📸 Source/Description: Structure for Complex IUPAC Naming Example

• Principal Functional Group: Ketone () → suffix '-one'.
• Parent Chain: 7 carbons including the ketone → heptanone.
• Numbering: Number from the right to give the ketone the lowest number (position 2).
• Substituents: A bromo group at position 5, a chloro group at position 4.
• Full Name (Alphabetical Order): 5-bromo-4-chloroheptan-2-one.

2.2 Aromatic Compounds: Benzene Derivatives

Aromatic compounds are a special class of cyclic, planar molecules with delocalized electrons that exhibit exceptional stability. The archetype is benzene (). For benzene rings with two substituents, relative positions are named using ortho- (o-), meta- (m-), or para- (p-).

📸 Source/Description: Figure 2.1: Ortho- (1,2), meta- (1,3), and para- (1,4) positions on a benzene ring relative to a substituent at position 1.

2.3 Key Functional Groups and Their Nomenclature

The functional group is the reactive part of a molecule and determines its chemical personality. The table below lists key groups for the IMAT in decreasing order of naming priority.

3.1 Core Concepts: Nucleophiles and Electrophiles

Nearly all organic reactions involve the interaction between an electron-rich species and an electron-poor species.

• Nucleophile ("nucleus loving"): An electron-rich species that donates an electron pair to form a new covalent bond. Nucleophiles are Lewis bases. Examples include species with lone pairs () or bonds (alkenes, alkynes).
• Electrophile ("electron loving"): An electron-poor species that accepts an electron pair. Electrophiles are Lewis acids. Examples include species with a positive charge () or a partial positive charge due to bond polarity ( on the carbon in ).

Organic chemistry can be seen as the story of nucleophiles attacking electrophiles. Identifying these roles in a reaction is the first step to understanding its mechanism.

3.2 Reaction Types Overview

• Addition: Two molecules combine to form a single larger molecule. This is characteristic of compounds with multiple bonds (alkenes, alkynes), where a bond breaks and two new bonds form.
• Elimination: The reverse of addition. One molecule splits into two smaller ones. Two bonds break, and a bond is formed. Dehydration of an alcohol is a classic example.
• Substitution: An atom or group in a molecule is replaced by another atom or group. This is common for alkanes (free-radical substitution) and alkyl halides (nucleophilic substitution).
• Rearrangement: A molecule undergoes a reorganization of its bonds and atoms to yield a structural isomer of the original molecule.

3.3 Nucleophilic Substitution Reactions ( and )

These reactions are fundamental for interconverting functional groups, typically involving an alkyl halide () and a nucleophile ().

The Reaction

Stands for Substitution, Nucleophilic, Bimolecular. It is a single-step concerted reaction. The nucleophile attacks the carbon atom from the side opposite to the leaving group (backside attack). This leads to an inversion of stereochemistry at the reaction center, known as a Walden inversion.

• Kinetics: Rate = k[Alkyl Halide][Nucleophile]. (Second order)
• Substrate: Favors unhindered substrates. . Tertiary () substrates do not react via due to steric hindrance.
• Stereochemistry: Complete inversion of configuration.

📸 Source/Description: Figure 3.1: The concerted, one-step mechanism of an SN2 reaction, showing the backside attack and inversion of stereochemistry.

The Reaction

Stands for Substitution, Nucleophilic, Unimolecular. It is a two-step reaction. The first and rate-determining step is the spontaneous dissociation of the leaving group to form a planar carbocation intermediate. In the second step, the nucleophile attacks the carbocation. Since the carbocation is planar, the nucleophile can attack from either face, leading to a mixture of retention and inversion products (racemization).

• Kinetics: Rate = k[Alkyl Halide]. (First order)
• Substrate: Favors substrates that form stable carbocations. . Methyl and primary () halides do not react.
• Stereochemistry: Racemization (mixture of inversion and retention).

📸 Source/Description: Figure 3.2: The two-step mechanism of an SN1 reaction, proceeding through a planar carbocation intermediate, leading to racemization.

3.4 Electrophilic Addition to Alkenes

The electron-rich bond of alkenes is a nucleophile and readily undergoes electrophilic addition. An electrophile attacks the bond, forming a carbocation intermediate, which is then attacked by a nucleophile.

Markovnikov's Rule: In the addition of H-X to an unsymmetrical alkene, the hydrogen atom adds to the carbon atom that already has more hydrogen atoms ("the rich get richer"). This is because the reaction proceeds via the most stable carbocation intermediate (tertiary > secondary > primary).

📸 Source/Description: Figure 3.3: Addition of HBr to propene. The major product is 2-bromopropane, formed via the more stable secondary carbocation.

3.5 Key Reactions of Functional Groups

Oxidation of Alcohols

The outcome depends on the class of alcohol and the strength of the oxidizing agent (e.g., ).

📸 Source/Description: Figure 3.4: Primary alcohols oxidize to aldehydes then to carboxylic acids with strong agents. Secondary alcohols oxidize to ketones. Tertiary alcohols are resistant to oxidation.

Fischer Esterification

A reversible, acid-catalyzed reaction between a carboxylic acid and an alcohol to produce an ester and water. It's an equilibrium process, and the yield of the ester can be increased by removing water as it is formed or by using an excess of one reactant.

Electrophilic Aromatic Substitution

This is the characteristic reaction of benzene and its derivatives. The stable aromatic ring is preserved. An electrophile () attacks the electron-rich ring, replacing a hydrogen atom. Common examples include nitration, halogenation, and Friedel-Crafts alkylation.

4.1 Amino Acids and Peptide Bonds

Amino acids are the building blocks (monomers) of proteins. They are characterized by a central alpha-carbon bonded to an amino group (), a carboxyl group (), a hydrogen atom, and a variable side chain (R group). At physiological pH (~7.4), they exist as zwitterions (dipolar ions) with a protonated amino group () and a deprotonated carboxyl group (). Amino acids link via peptide bonds (a type of amide linkage) in a dehydration synthesis reaction to form polypeptides.

📸 Source/Description: Figure 4.1: The formation of a dipeptide via a dehydration reaction, creating a peptide bond between the carboxyl group of one amino acid and the amino group of another.

4.2 Carbohydrates (Sugars)

Carbohydrates (saccharides) are polyhydroxy aldehydes or ketones, or substances that yield them upon hydrolysis. They serve as a primary energy source and structural components.

• Monosaccharides: Simple sugars like glucose, fructose, and galactose. In aqueous solution, they exist in equilibrium between a linear and a more stable cyclic form. Cyclization of glucose creates a new chiral center at C1 (the anomeric carbon), leading to two diastereomers called anomers (α and β).
• Disaccharides: Two monosaccharides joined by a glycosidic linkage. Examples: Sucrose (glucose + fructose), Lactose (galactose + glucose), Maltose (glucose + glucose).
• Polysaccharides: Polymers of monosaccharides. Examples: Starch (energy storage in plants), Glycogen (energy storage in animals), Cellulose (structural component in plants).

📸 Source/Description: Figure 4.2: The cyclization of D-glucose. The linear form closes to form two cyclic anomers, α-D-glucose and β-D-glucose, which differ only in the orientation of the -OH group at the anomeric carbon (C1).

4.3 Lipids

Lipids are a diverse group of naturally occurring molecules that are soluble in nonpolar organic solvents. They include fats, oils, waxes, steroids, and phospholipids.

• Fatty Acids: Long-chain carboxylic acids. They can be saturated (no C=C double bonds) or unsaturated (one or more C=C double bonds).
• Triglycerides (Fats and Oils): Triesters of glycerol and three fatty acids. They are the main form of energy storage in animals.
• Phospholipids: Similar to triglycerides, but one fatty acid is replaced by a phosphate group. Their amphipathic nature (hydrophilic head, hydrophobic tail) makes them the primary component of cell membranes.

While IUPAC nomenclature provides a systematic way to name compounds, many simple and historically significant organic compounds are still widely known by their common (trivial) names. Familiarity with these is essential for understanding questions in the IMAT and in general chemical literature.

Test your expanded knowledge with these practice questions covering all the key concepts discussed in this guide, from fundamental structures and nomenclature to reaction mechanisms and biomolecules.