Fundamental Principles of Organic Chemistry

Organic chemistry is the chemistry of carbon compounds. Carbon's tetravalency, ability to catenate, and capacity to form multiple bonds explain the diversity of more than ten million known organic compounds. The AAMC MCAT content outline expects fluency with classification of organic compounds, functional groups, and isomerism (including stereoisomerism).

AAMC content categories. This chapter covers three subtopics — definition and classification, functional groups, and isomerism (with emphasis on stereoisomerism). Memorize the functional-group table and the cis/trans & chirality basics.

Definition and Classification of Organic Compounds

An organic compound contains carbon, almost always hydrogen, and frequently O, N, S, halogens or P. (Oxides of carbon, carbonates, bicarbonates, cyanides and carbides are conventionally treated as inorganic.) Carbon's distinctive features — tetravalency, catenation, multiple-bond ability, and small atomic size — produce the unparalleled structural variety of organic chemistry.

Three structural classes

Aliphatic compounds

Open-chain (straight or branched) hydrocarbons and their derivatives. May be saturated (alkanes) or unsaturated (alkenes, alkynes). Examples: hexane, but-2-ene, propan-1-ol.

Alicyclic compounds

Carbocyclic but non-aromatic rings — behave chemically like aliphatic compounds. Examples: cyclohexane, cyclopentene, cyclopropane.

Aromatic compounds

Cyclic, planar molecules that obey Hückel's rule (4n + 2 π electrons). Show characteristic stability and prefer substitution to addition. Examples: benzene, toluene, naphthalene, pyridine.

Heterocyclic compounds

Cyclic compounds with at least one ring atom other than carbon (commonly N, O or S). Pyridine and furan are aromatic heterocycles; tetrahydrofuran is non-aromatic.

Functional Group

A functional group is the atom, group of atoms, or bond that determines the characteristic chemical reactions of a molecule. Members of a series sharing the same functional group form a homologous series — differing by −CH₂−, with similar chemical behavior and gradual physical-property changes.

High-yield functional groups for the MCAT

−OH (Hydroxyl): Alcohols (R−OH) and phenols (Ar−OH).
−CHO (Aldehyde): R−CHO — carbonyl with H attached. Suffix "-al".
>C=O (Ketone): R−CO−R′. Suffix "-one".
−COOH (Carboxylic acid): R−COOH. Suffix "-oic acid".
−COOR (Ester): R−COO−R′. Suffix "alkyl … -oate".
−CONH₂ (Amide): R−CONH₂. Suffix "-amide".
−NH₂ (Amine): R−NH₂ primary; R₂NH secondary; R₃N tertiary. Suffix "-amine".
−CN (Nitrile): R−C≡N. Suffix "-nitrile".
−NO₂ (Nitro): R−NO₂. Always a prefix.
−X (Halide): R−F, −Cl, −Br, −I. Always a prefix (fluoro-, chloro-, etc.).

Order of priority (suffix) in IUPAC naming

−COOH > −COOR > −CONH₂ > −CN > −CHO > >C=O > −OH > −NH₂. Higher-priority groups are named as the suffix; lower ones become prefixes.

Mnemonic for suffix priority. "Carboxylic Acids Excellently Crush Aldehydes Killing Other Amino Halides" → Acid > Ester > Amide > Nitrile > Aldehyde > Ketone > Alcohol > Amine > Halide.

Isomerism (Stereoisomerism)

Isomers share the same molecular formula but differ in arrangement of atoms. The two main branches are structural (constitutional) and stereo isomerism.

Structural (constitutional) isomerism

Chain isomers — differ in carbon skeleton (n-butane vs isobutane).
Position isomers — differ in position of a substituent or functional group (1-propanol vs 2-propanol).
Functional-group isomers — same formula, different functional group (ethanol C₂H₆O vs dimethyl ether).
Tautomers — constitutional isomers in rapid equilibrium that interconvert by moving a proton and a π bond (keto ⇌ enol). High-yield on the MCAT.

Stereoisomerism

Same atoms, same connectivity, different spatial arrangement. Two main classes: geometrical (cis/trans, E/Z) and optical (chirality).

Geometrical (cis/trans, E/Z)

Arises from restricted rotation about a C=C double bond or in a ring. cis = identical groups on the same side; trans = opposite sides. The E/Z system uses CIP priority: Z (zusammen) = higher-priority groups on same side; E (entgegen) = on opposite sides. Example: cis- and trans-2-butene have different boiling points and dipole moments.

Optical isomerism (chirality)

A molecule is chiral if it is non-superimposable on its mirror image. The most common cause is a carbon bonded to four different groups (a stereocenter). The two mirror-image forms are enantiomers — identical in physical and chemical properties except they rotate plane-polarized light in equal but opposite directions and behave differently in chiral environments. A 50:50 mixture is a racemic mixture (optically inactive).

Diastereomers & meso compounds

Diastereomers are stereoisomers that are not mirror images (they differ at some but not all stereocenters). Unlike enantiomers, they have different physical properties (melting point, boiling point, solubility) and can be separated by ordinary means. cis/trans (E/Z) isomers are one type of diastereomer. A molecule with n stereocenters has at most 2ⁿ stereoisomers.
A meso compound contains stereocenters but is achiral overall because it has an internal plane of symmetry — so it is optically inactive despite having stereocenters (e.g. meso-tartaric acid).

R/S (CIP) and (+/−) designations

R/S describes absolute configuration at a stereocenter using Cahn-Ingold-Prelog priority rules. Looking from the side opposite the lowest-priority group: clockwise = R (rectus); counterclockwise = S (sinister).
(+) / (−) describes the direction in which a sample rotates plane-polarized light: dextrorotatory (+) or levorotatory (−). There is no fixed correlation between R/S and (+)/(−) — they are independent labels.

Common trap. R/S and (+/−) are unrelated. An R isomer can be either dextrorotatory or levorotatory — the sign of rotation is an experimental fact, not a consequence of the configuration.

Worked MCQs

Five MCQs that capture the high-yield testing patterns for this chapter. Read every explanation — the deeper concept lives there.

Q1. A compound containing the −COOH group is named as a:

Aldehyde
Carboxylic acid
Ester
Ketone

−COOH (carboxyl) is a hydroxyl group attached to a carbonyl carbon and defines the carboxylic acid family (R−COOH). Its suffix "-oic acid" is the highest priority among common functional groups.

Q2. Which of the following is an example of functional-group isomerism?

n-butane and isobutane
1-propanol and 2-propanol
Ethanol and dimethyl ether
cis-2-butene and trans-2-butene

Both ethanol (C₂H₅OH) and dimethyl ether (CH₃OCH₃) share the molecular formula C₂H₆O but contain different functional groups (alcohol vs ether). The other pairs are chain, position and geometrical isomers respectively.

Q3. A carbon atom bonded to four different groups is described as:

Tertiary
Quaternary
Chiral / stereocenter
Aromatic

Such a carbon has no superimposable mirror image, giving rise to optical isomerism. It is termed a chirality center (or stereocenter). Tertiary and quaternary refer to the number of carbons attached, not chirality.

Q4. A 50:50 mixture of two enantiomers is called:

Diastereomeric mixture
Racemic mixture
Meso compound
Tautomeric mixture

A racemic (or racemate) mixture contains equal amounts of (+) and (−) enantiomers. Their optical rotations cancel out exactly, so the mixture is optically inactive even though each molecule is chiral.

Q5. Geometrical isomerism (cis/trans) is shown by:

n-butane
Methanol
2-butene
Ethyne

2-butene has restricted rotation about the C=C double bond and two different groups (H, CH₃) on each sp² carbon, giving rise to cis-2-butene and trans-2-butene. n-Butane has free rotation; ethyne has identical H atoms; methanol has no double bond.

Quick Recap

Organic compounds are classified as aliphatic (open chain), alicyclic (non-aromatic ring), aromatic (4n+2 π rings), or heterocyclic (ring contains N/O/S).
Functional groups dictate chemical behavior and IUPAC suffix.
Suffix priority: COOH > COOR > CONH₂ > CN > CHO > C=O > OH > NH₂.
Structural isomers: chain, position, functional group, tautomers.
Stereoisomers: geometrical (cis/trans, E/Z) and optical (R/S, +/−, enantiomers, racemic).
Enantiomers = non-superimposable mirror images; diastereomers = stereoisomers that are not mirror images (different physical properties). Meso compounds have stereocenters but are achiral (internal mirror plane).
Chirality requires four different groups on a carbon (no plane of symmetry).
R/S and (+)/(−) are independent — no fixed correlation.

Test yourself. Take a timed practice test or browse the topic-wise MCQs to lock these concepts in.