Introduction to Organic Chemistry

• Organic chemistry is the study of the structure, properties, composition, reactions, and preparation of carbon-containing compounds.
• These compounds may contain hydrogen, nitrogen, oxygen, halogens, phosphorus, silicon, and sulfur.
• It overlaps with many areas including medicinal chemistry, biochemistry, and petrochemistry.

Historical Context

• Originally defined as the chemistry of compounds produced by living organisms.
• Vitalism, the belief that organic compounds could only be formed by living things, was disproven in 1828 when Friedrich Wöhler synthesized urea from inorganic materials.
• Modern organic chemistry studies synthetic and naturally occurring compounds.

Core Principles

• Carbon's ability to form stable chains and rings with itself (catenation) and other elements allows for a vast diversity of structures
• Organic molecules are primarily held together by covalent bonds.
• Molecular structure and shape is critical in determining reactivity, physical properties, and biological function.
• Isomers are compounds with the same molecular formula but different structural formulas and properties.

Functional Groups

• Functional groups are specific atoms or groups of atoms within molecules that are responsible for characteristic chemical reactions.
• Common functional groups include:
  • Alkanes (C-C single bonds): Relatively unreactive, form the carbon backbone.
  • Alkenes (C=C double bonds): Undergo addition reactions.
  • Alkynes (C≡C triple bonds): Undergo addition reactions.
  • Alcohols (R-OH): Participate in hydrogen bonding; reactive towards oxidation and esterification.
  • Ethers (R-O-R'): Relatively unreactive; common solvents.
  • Aldehydes (R-CHO): Reactive towards oxidation and nucleophilic addition.
  • Ketones (R-CO-R'): Less reactive than aldehydes towards oxidation.
  • Carboxylic acids (R-COOH): Acidic; undergo esterification and amide formation.
  • Esters (R-COOR'): Formed from carboxylic acids and alcohols; common fragrances.
  • Amines (R-NH2, R2NH, R3N): Basic; react with acids.
  • Amides (R-CO-NR'2): Relatively stable; important in proteins and polymers.
  • Halides (R-X, where X = F, Cl, Br, I): Participate in substitution and elimination reactions.
  • Aromatic rings (e.g., benzene): Stable; undergo electrophilic aromatic substitution.

Isomerism

• Structural isomers have the same molecular formula but different connectivity.
• Stereoisomers have the same connectivity but different arrangement in space.
• Enantiomers are stereoisomers that are non-superimposable mirror images (chiral molecules).
• Diastereomers are stereoisomers that are not enantiomers.
• Cis-trans isomers (geometric isomers) occur when there is restricted rotation, such as in alkenes or cyclic compounds.

Reaction Mechanisms

• A reaction mechanism is a step-by-step sequence of elementary reactions describing the overall chemical change.
• Mechanisms involve the movement of electrons, often depicted with curved arrows.
• Common types of reactions include:
  • Addition: Two or more molecules combine to form a larger one.
  • Elimination: A molecule loses atoms or groups of atoms.
  • Substitution: An atom or group of atoms is replaced by another atom or group of atoms.
  • Rearrangement: A molecule undergoes a reorganization of its atoms and bonds.

Key Reaction Types

• SN1 Reactions: Unimolecular nucleophilic substitution; proceeds through a carbocation intermediate; favored by polar protic solvents and tertiary substrates.
• SN2 Reactions: Bimolecular nucleophilic substitution; concerted reaction; favored by polar aprotic solvents and primary substrates.
• E1 Reactions: Unimolecular elimination; proceeds through a carbocation intermediate; favored by strong acids and tertiary substrates; often competes with SN1.
• E2 Reactions: Bimolecular elimination; concerted reaction; requires anti-periplanar geometry; favored by strong bases and heat; often competes with SN2.
• Electrophilic Aromatic Substitution: Aromatic ring is attacked by an electrophile, followed by proton loss to regenerate the aromatic system.
• Addition Reactions: Reactions where two reactants add together to form a single product (e.g. hydrogenation, halogenation, hydration).
• Oxidation Reactions: Reactions that increase the number of bonds to oxygen or decrease the number of bonds to hydrogen.
• Reduction Reactions: Reactions that increase the number of bonds to hydrogen or decrease the number of bonds to oxygen.

Spectroscopy

• Techniques used to determine structure and properties of organic molecules
• NMR Spectroscopy: Provides information about the carbon-hydrogen framework of a molecule.
• IR Spectroscopy: Identifies functional groups based on vibrational modes.
• Mass Spectrometry: Determines the molecular weight and fragmentation pattern of a molecule.
• UV-Vis Spectroscopy: Analyzes electronic transitions, useful for conjugated systems.

Nomenclature

• IUPAC nomenclature provides a systematic way to name organic compounds.
• Identify the parent chain, number the chain, identify and name substituents, assign locants, and assemble the name.
• Common functional groups are assigned specific suffixes and prefixes.

Acids and bases

• Bronsted-Lowry acids donate protons, and Bronsted-Lowry bases accept protons.
• Lewis acids accept electron pairs, and Lewis bases donate electron pairs.
• The strength of an organic acid is related to the stability of its conjugate base. Factors affecting stability include inductive effects, resonance, and aromaticity.

Alkanes and Cycloalkanes

• Alkanes are saturated hydrocarbons with the general formula CnH2n+2.
• Cycloalkanes are cyclic saturated hydrocarbons with the general formula CnH2n.
• Conformational analysis: Study of different conformations of a molecule and their relative energies. Cyclohexane adopts a chair conformation to minimize steric strain.

Chirality

• A chiral molecule is non-superimposable on its mirror image.
• A chiral center is usually a carbon atom bonded to four different groups.
• Enantiomers rotate plane-polarized light in opposite directions.
• Racemic mixtures contain equal amounts of both enantiomers and are optically inactive.

Aromaticity

• Aromatic compounds are cyclic, planar, conjugated systems that obey Hückel's rule (4n+2 π electrons).
• Aromatic compounds are exceptionally stable due to delocalization of electrons.
• Common aromatic compounds include benzene and its derivatives.

Polymers

• Large molecules made up of repeating structural units (monomers).
• Addition polymers are formed by joining monomers together without loss of atoms.
• Condensation polymers are formed by joining monomers together with the loss of a small molecule such as water.
• Examples include polyethylene, polystyrene, nylon, and polyester.

Biomolecules

• Carbohydrates: Provide energy and structural support; include monosaccharides (e.g., glucose), disaccharides (e.g., sucrose), and polysaccharides (e.g., starch).
• Lipids: Include fats, oils, phospholipids, and steroids; provide energy storage, insulation, and cell membrane structure.
• Proteins: Made up of amino acids; perform a variety of functions, including catalysis, transport, and structural support.
• Nucleic acids: DNA and RNA; carry genetic information.

Laboratory Techniques

• Distillation separates liquids based on boiling points.
• Extraction separates compounds based on solubility.
• Chromatography separates compounds based on their interactions with a stationary and mobile phase.
• Recrystallization purifies solids based on solubility.

Reaction Rates

• Factors affecting reaction rates include concentration, temperature, and catalysts.
• Catalysts speed up reactions by lowering the activation energy.