👩🏽‍🔬Honors Chemistry Unit 12 – Organic Chemistry

Key Concepts and Definitions

• Organic chemistry focuses on the study of carbon-containing compounds and their properties, structures, and reactions
• Hydrocarbons consist of only carbon and hydrogen atoms and form the basis for many organic compounds (alkanes, alkenes, alkynes)
• Functional groups are specific arrangements of atoms within a molecule that give it distinct chemical properties (hydroxyl, carboxyl, amino)
• Isomers are compounds with the same molecular formula but different structural or spatial arrangements
  • Structural isomers have different bonding arrangements between atoms
  • Stereoisomers have the same bonding but different 3D orientations (enantiomers, diastereomers)
• Reaction mechanisms describe the step-by-step process by which reactants are converted into products, including the formation and breaking of bonds and the movement of electrons
• Synthesis involves the creation of complex organic molecules from simpler building blocks, while analysis techniques are used to determine the structure and composition of organic compounds (NMR, IR, mass spectrometry)
• Organic compounds play a crucial role in various real-world applications, including pharmaceuticals, plastics, fuels, and biochemistry

Carbon's Unique Properties

• Carbon has four valence electrons, allowing it to form stable covalent bonds with up to four other atoms
• The ability of carbon to form strong, stable bonds with itself and other elements enables the creation of a wide variety of organic compounds
• Carbon can form single, double, or triple bonds, leading to diverse molecular structures (alkanes, alkenes, alkynes)
• The tetrahedral geometry of carbon atoms allows for the formation of three-dimensional structures and stereoisomers
• Carbon's electronegativity is intermediate, enabling it to form polar and nonpolar bonds depending on the attached atoms
• The relatively small size of carbon atoms allows for compact and efficient packing in organic molecules
• Carbon's ability to form stable bonds with other carbon atoms leads to the creation of long chains, branched structures, and cyclic compounds

Bonding and Molecular Structure

• Covalent bonding involves the sharing of electrons between atoms to form stable molecules
• Sigma (σ) bonds are formed by the direct overlap of atomic orbitals along the internuclear axis, resulting in a single bond (C-C, C-H)
• Pi (π) bonds are formed by the sideways overlap of p orbitals, resulting in double or triple bonds (C=C, C≡C)
  • Double bonds consist of one σ and one π bond, while triple bonds have one σ and two π bonds
• Hybridization describes the mixing of atomic orbitals to form new hybrid orbitals with specific geometries (sp³, sp², sp)
  • sp³ hybridization results in tetrahedral geometry (methane)
  • sp² hybridization leads to trigonal planar geometry (ethene)
  • sp hybridization produces linear geometry (ethyne)
• Molecular geometry is determined by the arrangement of atoms and the presence of lone pairs (VSEPR theory)
• Polarity of molecules depends on the distribution of charge and the presence of polar bonds (dipole moments)

Functional Groups and Their Reactions

• Alcohols contain a hydroxyl group (-OH) and can undergo dehydration to form alkenes or oxidation to form aldehydes or ketones
• Aldehydes and ketones have a carbonyl group (C=O), with aldehydes having the carbonyl at the end of a carbon chain and ketones having it within the chain
  • Aldehydes and ketones can be reduced to alcohols or oxidized to carboxylic acids
• Carboxylic acids have a carboxyl group (-COOH) and can form esters through condensation reactions with alcohols or be reduced to aldehydes
• Amines contain a nitrogen atom bonded to carbon and can act as bases, forming salts with acids or participating in nucleophilic substitution reactions
• Ethers have an oxygen atom bonded to two carbon atoms and are relatively unreactive but can undergo cleavage reactions
• Esters are formed by the condensation of a carboxylic acid and an alcohol, releasing water as a byproduct
• Amides are derived from carboxylic acids, with the hydroxyl group replaced by an amino group (-NH₂), and are common in proteins and peptides

Isomerism and Stereochemistry

• Structural isomers have the same molecular formula but different bonding arrangements between atoms (butane, isobutane)
• Stereoisomers have the same bonding but different 3D orientations of atoms in space
  • Enantiomers are non-superimposable mirror images of each other and have opposite optical activity (levorotatory, dextrorotatory)
  • Diastereomers are stereoisomers that are not mirror images and have different physical properties
• Chirality refers to the property of a molecule being non-superimposable on its mirror image, often due to the presence of an asymmetric carbon atom (chiral center)
• The absolute configuration of a chiral center is designated using the R/S system, based on the priority of attached groups (Cahn-Ingold-Prelog rules)
• Optical activity is the ability of a chiral compound to rotate plane-polarized light, with the direction and magnitude dependent on the specific enantiomer
• Racemic mixtures contain equal amounts of both enantiomers and do not exhibit optical activity
• Diastereomers can have different reactivity and biological activity, making stereochemistry crucial in drug design and synthesis

Reaction Mechanisms

• Reaction mechanisms provide a detailed, step-by-step description of how reactants are converted into products
• Nucleophiles are electron-rich species that donate an electron pair to form a new bond, while electrophiles are electron-poor species that accept an electron pair
• Substitution reactions involve the replacement of one atom or group by another, with the mechanism dependent on the substrate and conditions (SN1, SN2)
  • SN1 reactions proceed through a carbocation intermediate and are unimolecular
  • SN2 reactions involve a concerted backside attack by the nucleophile and are bimolecular
• Elimination reactions result in the formation of a double bond and the loss of a small molecule (usually water or hydrogen halide), with the mechanism dependent on the substrate and conditions (E1, E2)
• Addition reactions involve the addition of atoms or groups across a double or triple bond, with the mechanism dependent on the substrate and reagents (electrophilic, nucleophilic)
• Rearrangements involve the intramolecular transfer of atoms or groups within a molecule, often driven by the formation of a more stable product (carbocation rearrangements)
• Radical reactions involve the formation and propagation of highly reactive species with unpaired electrons, often initiated by light or heat (halogenation, polymerization)

Synthesis and Analysis Techniques

• Retrosynthetic analysis involves working backward from a target molecule to identify simpler starting materials and the reactions needed to synthesize the target
• Functional group interconversion is the process of converting one functional group into another using specific reagents and conditions (oxidation, reduction, protection)
• Multistep synthesis requires careful planning and execution of a series of reactions to build complex molecules from simpler starting materials
• Purification techniques are used to isolate and purify the desired product from a reaction mixture (recrystallization, distillation, chromatography)
• Spectroscopic methods provide structural information about organic compounds based on their interaction with electromagnetic radiation
  • Nuclear Magnetic Resonance (NMR) spectroscopy reveals the chemical environment of specific nuclei (¹H, ¹³C) and helps determine molecular structure
  • Infrared (IR) spectroscopy identifies functional groups based on their characteristic absorption of infrared light
  • Mass spectrometry determines the molecular mass and fragmentation pattern of a compound, aiding in structure elucidation
• Chromatographic techniques separate mixtures based on the differential interaction of components with a stationary and mobile phase (TLC, GC, HPLC)

Real-World Applications

• Pharmaceuticals are a major application of organic chemistry, with many drugs being small organic molecules that target specific biological receptors or enzymes
  • Drug discovery involves the identification of lead compounds and optimization of their structure and properties to improve efficacy and reduce side effects
  • Synthesis of complex natural products and their analogs has led to the development of numerous life-saving medications (antibiotics, anticancer agents)
• Plastics and polymers are ubiquitous materials derived from organic monomers, with properties tailored for specific applications (packaging, textiles, construction)
  • Polymerization reactions, such as addition and condensation polymerization, create long-chain macromolecules with repeating units
  • Biodegradable and renewable plastics are being developed to address environmental concerns and sustainability
• Petrochemicals and fuels are derived from the processing of crude oil and natural gas, which are composed primarily of hydrocarbons
  • Fractional distillation separates crude oil into various fractions based on boiling point, which are then further processed into fuels, lubricants, and feedstocks for the chemical industry
  • Catalytic cracking and reforming processes convert long-chain hydrocarbons into shorter, more valuable products (gasoline, aromatic compounds)
• Biochemistry is the study of chemical processes within living organisms, with organic compounds playing a central role in the structure and function of biomolecules
  • Proteins are polymers of amino acids that serve various functions, such as catalysis (enzymes), transport, and structural support
  • Nucleic acids (DNA and RNA) store and transmit genetic information, with their structure and function dependent on the sequence of nucleotide bases
  • Carbohydrates are important energy sources and structural components, with monosaccharides serving as building blocks for larger polysaccharides (starch, cellulose)
  • Lipids, including fats, oils, and steroids, play roles in energy storage, cell membranes, and signaling