Organic Chemistry Fundamentals — Structure, Bonding, and the Carbon Atom

🟢 Lite — Quick Review (1h–1d)

Rapid summary for last-minute revision before your exam.

Organic chemistry is the study of carbon-containing compounds. The unique ability of carbon to form four covalent bonds and to chain, branch, or ring with itself makes organic chemistry vast. For SLMC, focus on understanding why carbon is special, the types of bonds it forms, functional groups, and the distinction between organic and inorganic compounds.

High-Yield Facts for SLMC:

• Carbon has atomic number 6: electronic configuration 1s² 2s² 2p² — forms 4 bonds
• Organic compounds contain carbon + hydrogen ± oxygen, nitrogen, halogens, sulfur, or phosphorus
• Catenation: carbon’s ability to form long chains with itself (key to organic diversity)
• Tetravalence: carbon always forms 4 bonds (single, double, or triple)
• ⚡ Exam tip: If a compound has carbon, it is presumed organic UNLESS it contains carbonate (CO₃²⁻), bicarbonate, cyanide, cyanate, or is a simple oxide of carbon (CO, CO₂) — these are inorganic

---

🟡 Standard — Regular Study (2d–2mo)

Standard content for students with a few days to months.

Organic Chemistry Fundamentals — SLMC Medical (Sri Lanka) Study Guide

Why Carbon Is the Backbone of Organic Chemistry

Carbon occupies Group 14 of the periodic table. With 4 valence electrons, it needs 4 more to complete its octet — so it forms 4 covalent bonds. Unlike metals that lose/gain electrons (ionic bonding), carbon shares electrons, creating strong directional covalent bonds.

Key properties of carbon that make it unique:

• Tetravalence: Four valence electrons → four bonds per carbon atom
• Catenation: C–C bonds are strong (~347 kJ/mol), allowing long chains, branched structures, and rings
• Multiple bonding: Carbon forms double bonds (C=C) and triple bonds (C≡C)
• Small atomic radius: Allows effective orbital overlap for strong σ and π bonds

Bonding in Organic Molecules

Single Bonds (σ bonds)

• Sp³ hybridized carbon (e.g., methane CH₄, ethane C₂H₆)
• sigma (σ) bond: head-on overlap of orbitals → free rotation around the bond axis
• Bond angle: ~109.5° (tetrahedral geometry)

Double Bonds (σ + π)

• sp² hybridized carbon (e.g., ethene C₂H₄)
• One σ bond + one π bond (lateral overlap of p-orbitals)
• No free rotation around C=C axis → geometric (cis/trans) isomerism

Triple Bonds (σ + 2π)

• sp hybridized carbon (e.g., ethyne C₂H₂)
• One σ bond + two π bonds
• Linear geometry (180° bond angle)

Hybridization Summary

Hybridization	Geometry	Bond Angle	Example
sp³	Tetrahedral	109.5°	CH₄, C₂H₆
sp²	Trigonal planar	120°	C₂H₄, benzene
sp	Linear	180°	C₂H₂, HCN

Structural Formulas

Molecular formula: Shows all atoms (e.g., C₄H₁₀ for butane) Condensed structural formula: Groups atoms (e.g., CH₃–CH₂–CH₂–CH₃) Full structural formula: Shows all bonds explicitly

Homologous Series

A homologous series is a family of organic compounds with:

1. Same general formula
2. Similar structural features (same functional group)
3. Gradual change in physical properties as molecular size increases
4. Similar chemical properties

Examples:

• Alkanes: CₙH₂ₙ₊₂
• Alkenes: CₙH₂ₙ
• Alcohols: CₙH₂ₙ₊₁OH

Functional Groups — The Heart of Organic Chemistry

A functional group is a specific atom or group of atoms within a molecule responsible for its characteristic chemical behavior.

Functional Group	Structure	Suffix	Example
Alkane	C–C (only C, H)	-ane	Butane
Alkene	C=C	-ene	Butene
Alkyne	C≡C	-yne	Butyne
Alcohol	–OH	-ol	Ethanol
Aldehyde	–CHO	-al	Acetaldehyde
Ketone	–CO–	-one	Acetone
Carboxylic acid	–COOH	-oic acid	Acetic acid
Amine	–NH₂	-amine	Methylamine
Ether	C–O–C	ether	Dimethyl ether
Halide	–Cl, –Br, etc.	halo-	Chloromethane

Key Definitions

• Homolysis: Bond breaks equally → two free radicals
• Heterolysis: Bond breaks unequally → carbocation (positive) + anion (negative) or vice versa
• Electrophile: Electron-pair acceptor (e.g., H⁺, NO₂⁺)
• Nucleophile: Electron-pair donor (e.g., OH⁻, CN⁻)
• Carbocation: Carbon with only 6 electrons (sp²), positively charged — unstable
• Carbanion: Carbon with 8 electrons and a negative charge (sp³)

Common Reactions in Organic Chemistry

Combustion (applies to all organic compounds containing C and H):

• Complete: CₙHₘ + (n + m/4)O₂ → nCO₂ + (m/2)H₂O
• Methane: CH₄ + 2O₂ → CO₂ + 2H₂O

Free radical halogenation of alkanes:

• CH₄ + Cl₂ → CH₃Cl + HCl (in UV light)
• Mechanism: Initiation → Propagation → Termination

Addition reactions (alkenes/alkynes):

• H₂ + alkene → alkane (hydrogenation, Ni catalyst)
• HX addition follows Markovnikov’s rule

How to Approach Organic Chemistry Questions in SLMC

1. Identify the functional group first — this determines the compound’s reactions
2. Check the hybridization — sp³ (single bonds), sp² (double), sp (triple)
3. Name the compound using IUPAC rules (more in Topic 3)
4. Check for isomerism — structural or geometric isomers affect properties (more in Topic 4)
5. Remember the reagent — acidified KMnO₄ oxidizes alkenes; bromine water decolorizes alkenes; Na/NaOH + heat affects halides

⚡ Exam tip: When asked “which compound is most reactive?”, look for the most unstable electron arrangement — an alkene is more reactive than an alkane because of the π electron cloud above/below the double bond waiting to react. For nucleophilic substitution, methyl halides react fastest (least steric hindrance), tertiary halides are slowest via SN1.

---

🔴 Extended — Deep Study (3mo+)

Comprehensive coverage for students on a longer study timeline.

Organic Chemistry Fundamentals — Comprehensive SLMC Medical (Sri Lanka) Notes

Electronic Effects in Organic Molecules

Understanding electron distribution is critical for predicting reaction outcomes:

Inductive Effect

• Polarity transmitted through σ bonds
• Electron-donating groups (EDG): –CH₃, –OH, –NH₂
• Electron-withdrawing groups (EWG): –NO₂, –CN, –COOH, –COOR, –CX₃
• Effect decreases with distance:影响力 at carbon-1 > carbon-2 > carbon-3

Resonance Effect

• Delocalization of π electrons or lone pairs through conjugated systems
• Stabilizes molecules (e.g., benzene, carboxylate ion)
• EWG via resonance: –NO₂, –COOH, –COOR, –CN, –SO₃H
• EDG via resonance: –OH, –NH₂, –OR, –NHR

Hyperconjugation

• Delocalization of σ electrons (C–H or C–C) into adjacent empty or π orbitals
• Explains stability of carbocations (more α-hydrogens = more stable)
• Order of carbocation stability: tertiary > secondary > primary > methyl

Stereochemistry Fundamentals

Chirality: A molecule is chiral if it is non-superimposable on its mirror image (like left and right hands). The carbon atom attached to four different groups is a stereocenter or chiral center.

Enantiomers: Non-superimposable mirror-image isomers. They rotate plane-polarized light in opposite directions.

R/S Nomenclature:

1. Assign priorities to four groups (highest atomic number = priority 1)
2. Orient lowest priority away from viewer
3. Trace 1→2→3: clockwise = R (rectus), counterclockwise = S (sinister)

D/L Nomenclature (older system):

• Glyceraldehyde is the reference compound
• Not the same as R/S (depends on carbon skeleton, not three-dimensional arrangement)

Thermodynamic vs Kinetic Control

In competing reactions (e.g., addition of HBr to butadiene):

• Kinetic product: Forms faster — less stable product; 1,2-addition product
• Thermodynamic product: Forms slower but is more stable; 1,4-addition product at higher temperature

Oxidation and Reduction in Organic Chemistry

Oxidation: Increase in oxygen content or decrease in hydrogen content

• Primary alcohol → aldehyde → carboxylic acid
• Secondary alcohol → ketone
• Alkane → CO₂ (complete oxidation = combustion)

Reduction: Decrease in oxygen content or increase in hydrogen content

• Alkene → alkane (H₂, Ni)
• Alkyne → alkane (H₂, Ni, or Na/NH₃ for trans-alkene)
• Carbonyl → alcohol (NaBH₄ or LiAlH₄)

Practice Question Patterns for SLMC

1. “Which carbon is sp² hybridized in CH₃–CH=CH₂?” → Answer: the middle carbon (CH)
2. “The bond angle in an sp-hybridized carbon is:” → 180°
3. “The functional group –COOH is:” → Carboxylic acid
4. “Which compound is chiral?” → Look for a carbon with four different substituents (e.g., 2-butanol: CH₃–CHOH–CH₂–CH₃ — the CHOH carbon is chiral)

Common Traps and Pitfalls

• Confusing molecular formula with structural formula
• Forgetting that CO, CO₂, carbonates, and cyanides are INORGANIC
• Assuming all organic compounds are natural (many are synthetic)
• Misidentifying functional groups — aldehyde (–CHO) is different from ketone (–CO–)
• Thinking all chiral carbons are asymmetric — need 4 different groups

---

Content adapted based on your selected roadmap duration. Switch tiers using the selector above.