organic-chemistry

# Organic Chemistry

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

## Why Carbon is Special

| 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.

## 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

1. Find the longest continuous carbon chain — this is the parent name.
2. Number the chain from the end nearest the first substituent.
3. Name substituents as prefixes with their position numbers.
4. Use di-, tri-, tetra- for multiple identical substituents.
5. 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.

**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.

### Worked Example: SN2 vs. SN1 Prediction

**Problem.** Predict the mechanism for: CH3Br + OH- -> CH3OH + Br-

**Analysis.** Substrat