Carbon chemistry, functional groups, IUPAC nomenclature, isomerism, reaction mechanisms (substitution, elimination, addition), polymers, and biochemistry basics. Covers hydrocarbon classes (alkanes, alkenes, alkynes, aromatics), common functional groups (alcohols, aldehydes, ketones, carboxylic acids, esters, amines, amides), stereochemistry, condensation and addition polymerization, and the four biomolecule classes (carbohydrates, lipids, proteins, nucleic acids). Use when analyzing organic structures, predicting reaction products, or connecting chemistry to biology.
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)
Concept IDs: chem-polymers, chem-biochemistry-basics
| Property | Consequence |
|---|---|
| 4 valence electrons, forms 4 bonds | 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.
| 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.
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.
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 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.
Same molecular formula, different connectivity. C4H10 has two structural isomers: butane (straight chain) and 2-methylpropane (branched).
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).
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).
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.
SN1 (unimolecular nucleophilic substitution): Two steps. (1) Leaving group departs, forming carbocation. (2) Nucleophile attacks. Rate = k[substrate]. Favored by: tertiary substrate (stable carbocation), polar protic solvent. Produces racemic mixture.
Problem. Predict the mechanism for: CH3Br + OH- -> CH3OH + Br-
Analysis. Substrate is primary (methyl — no branching). Strong nucleophile (OH-). Backside attack is unhindered. This is textbook SN2.
Problem. Predict the mechanism for: (CH3)3CBr + H2O -> (CH3)3COH + HBr
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.
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).
Alkene addition. Electrophilic addition to C=C:
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.
Monomers with C=C bonds undergo chain addition. No atoms are lost.
Example: Polyethylene. n CH2=CH2 -> -(CH2-CH2)n-
Other addition polymers: polypropylene (PP), polystyrene (PS), polyvinyl chloride (PVC), polytetrafluoroethylene (PTFE/Teflon).
Monomers with two functional groups react, releasing a small molecule (usually H2O) at each step.
Example: Nylon 6,6. Hexamethylenediamine (H2N-(CH2)6-NH2) + adipic acid (HOOC-(CH2)4-COOH) -> amide bonds (-CONH-) + H2O at each linkage.
Example: Polyester (PET). Ethylene glycol + terephthalic acid -> ester bonds (-COO-) + H2O.
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.
The four classes of biomolecules are all organic:
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).
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).
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).
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).
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.
H2N-CH2-CO-NH-CH(CH3)-COOH + H2O -> H2N-CH2-COOH + H2N-CH(CH3)-COOH
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.
| 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 |