Organic chemistry is the study of carbon-containing compounds and their reactions. Carbon's ability to form four stable covalent bonds, catenate (bond to itself in chains and rings), and hybridize in three ways (sp3, sp2, sp) generates an essentially infinite diversity of molecular architectures. This skill covers hydrocarbon families, functional groups, nomenclature, reaction mechanisms, polymers, and the biochemistry of life's molecules.
Agent affinity: pauling (bonding/molecular chemistry, primary for mechanisms and structure), franklin (materials/applied chemistry, for polymer and materials topics)
Tetrahedral (sp3), trigonal planar (sp2), or linear (sp) geometries
Similar electronegativity to H, O, N
Forms stable covalent bonds with life's key elements
Strong C-C bonds (347 kJ/mol)
Chains of hundreds to millions of carbons are stable
Multiple bond capability (C=C, C-triple-C)
Rigidity, planarity, and reactivity variation
Over 20 million organic compounds are known — dwarfing all inorganic compounds combined.
Hydrocarbon Families
Family
General formula
Bonding
Hybridization
Saturation
Alkanes
CnH(2n+2)
All single bonds
sp3
Saturated
Cycloalkanes
CnH(2n)
All single bonds, ring
sp3
Saturated
Alkenes
CnH(2n)
One C=C double bond
sp2 at C=C
Unsaturated
Alkynes
CnH(2n-2)
One C-triple-C triple bond
sp at triple bond
Unsaturated
Aromatics
Variable
Delocalized pi ring
sp2
Unsaturated
Benzene (C6H6) is the archetypal aromatic. Its 6 pi electrons are delocalized across the ring, creating exceptional stability (aromaticity). The resonance energy of benzene is approximately 150 kJ/mol — it does not undergo the addition reactions typical of alkenes.
IUPAC Nomenclature
Alkane Naming Rules
Find the longest continuous carbon chain — this is the parent name.
Number the chain from the end nearest the first substituent.
Name substituents as prefixes with their position numbers.
Use di-, tri-, tetra- for multiple identical substituents.
List substituents alphabetically (ignoring di-, tri- prefixes).
Worked Example: Naming a Branched Alkane
Structure: A 6-carbon chain with methyl groups on carbons 2 and 4.
Step 1. Parent chain: hexane (6 carbons).
Step 2. Number from the end that gives the lowest locants: positions 2 and 4 (not 3 and 5).
Step 3. Two methyl substituents at positions 2 and 4.
Name: 2,4-dimethylhexane.
Worked Example: Naming an Alkene
Structure: A 5-carbon chain with a double bond between carbons 1 and 2, and a methyl group on carbon 3.
Step 1. Parent chain includes the double bond: pentene.
Step 2. Number from the end nearest the double bond: 1-pentene.
Step 3. Methyl at position 3.
Name: 3-methyl-1-pentene.
Functional Groups
Functional groups are the reactive sites of organic molecules. They determine chemical behavior.
Group
Structure
Found in
Example
Hydroxyl
-OH
Alcohols
Ethanol (CH3CH2OH)
Carbonyl
C=O
Aldehydes (terminal), ketones (internal)
Formaldehyde (HCHO), acetone (CH3COCH3)
Carboxyl
-COOH
Carboxylic acids
Acetic acid (CH3COOH)
Ester
-COO-
Esters
Ethyl acetate (CH3COOCH2CH3)
Amino
-NH2
Amines
Methylamine (CH3NH2)
Amide
-CONH2
Amides
Acetamide (CH3CONH2)
Ether
-O-
Ethers
Diethyl ether (CH3CH2OCH2CH3)
Halide
-X (F, Cl, Br, I)
Alkyl halides
Chloromethane (CH3Cl)
Thiol
-SH
Thiols
Ethanethiol (CH3CH2SH)
Phosphate
-OPO3^2-
Phosphoesters
ATP, DNA backbone
Priority for naming: carboxylic acid > ester > amide > aldehyde > ketone > alcohol > amine. The highest-priority group becomes the suffix; lower-priority groups are prefixes.
Isomerism
Structural (Constitutional) Isomers
Same molecular formula, different connectivity. C4H10 has two structural isomers: butane (straight chain) and 2-methylpropane (branched).
Geometric (Cis-Trans) Isomers
Arise from restricted rotation around C=C double bonds. Cis: identical groups on the same side. Trans: on opposite sides. For more complex cases, use E/Z notation based on Cahn-Ingold-Prelog priority rules (higher atomic number = higher priority; Z = same side, E = opposite).
Worked example.2-butene has cis and trans isomers.
cis-2-butene: both CH3 groups on the same side of the double bond. Boiling point: 3.7 C.
trans-2-butene: CH3 groups on opposite sides. Boiling point: 0.9 C.
The cis isomer has a higher boiling point because it has a net dipole moment (polar); the trans isomer's dipoles cancel (nonpolar).
Enantiomers (Optical Isomers)
Mirror-image molecules that are non-superimposable. Require a chiral center — typically a carbon bonded to four different groups. Enantiomers have identical physical properties except they rotate plane-polarized light in opposite directions. They can have dramatically different biological activity (thalidomide: one enantiomer treats nausea, the other causes birth defects).
Reaction Mechanisms
Substitution Reactions
SN2 (bimolecular nucleophilic substitution): One step. Nucleophile attacks as leaving group departs. Backside attack causes inversion of configuration. Rate = k[substrate][nucleophile]. Favored by: strong nucleophile, primary substrate, polar aprotic solvent.
Analysis. Substrate is tertiary (three methyl groups block backside attack). Weak nucleophile (H2O). The t-butyl carbocation (CH3)3C+ is stable (three hyperconjugating methyls). This is SN1.
Elimination Reactions
E2: One step. Strong base removes a proton while the leaving group departs. Anti-periplanar geometry required. Competes with SN2 (use bulky base to favor E2).
E1: Two steps via carbocation. Competes with SN1. Zaitsev's rule: the more substituted alkene is the major product (more stable).
Addition Reactions
Alkene addition. Electrophilic addition to C=C:
HX addition: Markovnikov's rule — H adds to the carbon with more hydrogens. Anti-Markovnikov with peroxide (radical mechanism).
Halogenation (Br2): adds across double bond, anti-addition.
Hydration (H2O/H+): Markovnikov addition of OH.
Hydrogenation (H2/Pt): syn-addition, converts alkene to alkane.
Worked Example: Markovnikov Addition
Problem. Predict the major product of HBr addition to propene (CH3CH=CH2).
Step 1. H+ adds to the less-substituted carbon (CH2 end), forming a secondary carbocation on the middle carbon: CH3CH+CH3.
Step 2. Br- attacks the carbocation: CH3CHBrCH3 (2-bromopropane).
Markovnikov's rule in modern terms: the electrophile (H+) adds to form the more stable carbocation intermediate. Secondary > primary carbocation stability explains the regiochemistry.
Polymers
Addition (Chain-Growth) Polymers
Monomers with C=C bonds undergo chain addition. No atoms are lost.
Problem. Classify the polymerization of styrene (C6H5CH=CH2).
Analysis. Styrene has a C=C double bond. The pi bond opens and monomers chain-link. No small molecule is released. This is addition polymerization, producing polystyrene.
Problem. Classify the formation of a polyamide from a diamine and a diacid.
Analysis. Each linkage forms an amide bond and releases H2O. Two different functional groups react. This is condensation polymerization.
Biochemistry Basics
The four classes of biomolecules are all organic:
Carbohydrates
Monomers: Monosaccharides (glucose C6H12O6, fructose, galactose).
Polymers: Disaccharides (sucrose, lactose), polysaccharides (starch, cellulose, glycogen).
Bond: Glycosidic linkage (C-O-C between sugar units). Formed by condensation; broken by hydrolysis.
Function: Energy storage (starch, glycogen), structural (cellulose in plant cell walls).
Lipids
Not true polymers — diverse hydrophobic molecules. Fats/oils = glycerol + 3 fatty acids (ester bonds). Phospholipids = glycerol + 2 fatty acids + phosphate group (cell membranes). Steroids = four fused rings (cholesterol, hormones).
Saturated vs. unsaturated: Saturated fatty acids have no C=C bonds (solid at RT). Unsaturated have one or more C=C (liquid at RT, kinked chains reduce packing).
Proteins
Monomers: 20 amino acids (H2N-CHR-COOH), each with a unique R group.
Bond: Peptide bond (amide linkage, -CO-NH-) formed by condensation.
Levels of structure: Primary (sequence), secondary (alpha-helix, beta-sheet from H-bonding), tertiary (3D fold from R-group interactions), quaternary (multi-subunit assembly).
Function: Enzymes (catalysis), structural (collagen, keratin), transport (hemoglobin), immune (antibodies).
Nucleic Acids
Monomers: Nucleotides (sugar + phosphate + nitrogenous base).
DNA: Deoxyribose sugar. Bases: A, T, G, C. Double helix with complementary base pairing (A-T, G-C via hydrogen bonds).
RNA: Ribose sugar. Bases: A, U, G, C. Single-stranded.
Bond: Phosphodiester linkage (sugar-phosphate backbone).
Function: DNA stores genetic information. RNA translates it into proteins (mRNA, tRNA, rRNA).
Worked Example: Hydrolysis of a Dipeptide
Problem. What products form when the dipeptide Gly-Ala is hydrolyzed?
Reaction. The peptide bond (-CO-NH-) between glycine and alanine is broken by adding water.
Products: glycine and alanine (the two free amino acids). This is the reverse of condensation — the water molecule that was lost during peptide bond formation is restored.
Common Mistakes
Mistake
Why it fails
Fix
Ignoring carbon's implicit hydrogens
Structural formulas often omit H atoms
Each carbon forms 4 bonds total; fill remaining with H
Markovnikov without considering carbocation stability
The rule is about the intermediate, not memorized patterns
Always identify which carbocation is more stable
Confusing SN1/SN2 conditions
Wrong mechanism predicts wrong stereochemistry and product
Check substrate class (primary vs. tertiary), nucleophile strength, solvent
Writing 5 bonds on carbon
Carbon NEVER exceeds 4 bonds (no expanded octet)
Count bonds carefully in every structure
Confusing structural and geometric isomers
Structural = different connectivity; geometric = same connectivity, different spatial arrangement
Ask: are the atoms connected the same way?
Treating condensation and addition polymers the same
Different mechanisms, different properties
Condensation releases small molecules; addition does not
Cross-References
pauling agent: Molecular structure, bonding, and reaction mechanisms. Primary agent for organic structure and mechanism problems.
franklin agent: Polymer science and materials applications of organic chemistry.
