Smell a freshly peeled orange and then a handful of caraway seeds. Two different smells, from two molecules that have exactly the same atoms connected in exactly the same order. The only difference is that one is the mirror image of the other, like a left and right hand, and your nose can tell them apart. Spearmint and caraway are the same way: one handed form of carvone smells of spearmint, its mirror image of caraway.
Organic chemistry is the chemistry of carbon compounds, and it is the subject people fear most. It shouldn't be. It looks like thousands of reactions to memorise, but graduates carry something much smaller: a handful of shapes, a handful of small groups of atoms, and one idea about where electrons want to go. With those, reactions that look new are variations on ones you already know.
Carbon has four outer electrons and wants four bonds. In the molecule methane, CH₄, the four bonds point to the corners of a tetrahedron, 109.5° apart. That puzzled early chemists, because carbon's outer orbitals are one s and three p, which should not give four equal bonds. The fix is hybridisation: mix the s and p orbitals into four identical sp³ hybrids that point to the tetrahedron's corners. Jacobus van 't Hoff, in a pamphlet of 1874, proposed this tetrahedral carbon; Joseph Le Bel is credited with the same idea at the same time.
Mix fewer orbitals and you get different shapes. In ethene, each carbon uses one s and two p orbitals to make three sp² hybrids in a plane, 120° apart, and the leftover p orbital sticks up and down to form a pi bond over the top. In ethyne (acetylene) each carbon makes two sp hybrids in a line, 180° apart, and keeps two p orbitals for two pi bonds. The bond length and strength follow: single C–C about 153 pm and 347 kJ/mol; C=C about 133 pm and 611 kJ/mol; C≡C about 118 pm and 839 kJ/mol. Shorter and stronger as more electrons are shared, but not in simple proportion: a pi bond is weaker than a sigma bond.
Bond lengths and strengths as quoted for alkanes, alkenes and alkynes in Wikipedia's Alkene and Alkyne articles (citing March's Advanced Organic Chemistry); benzene's 140 pm from neutron diffraction. s character is 1 part in the number of orbitals mixed (25, 33, 50 %). Drawn schematically; the dashed bond points away from you.
In 1865 August Kekulé proposed that benzene is a ring; later work showed that all six bonds are the same length, 140 pm, between a single and a double bond. We will see why in the resonance section.
A big organic molecule is a skeleton of carbon and hydrogen, which is mostly inert, hung with a few small clusters of other atoms: a functional group. The skeleton sets the size and shape; the groups do the chemistry. An alcohol (–OH), a carboxylic acid (–COOH), an ester (–COO–), an amine (–NH₂), a ketone (C=O between carbons), an alkene (C=C): each behaves the same way wherever it appears. Learn about a dozen and you can read the structure of aspirin, a fruit flavour or a protein and know where the reactive spots are.
A small, illustrative list of familiar molecules, each tagged with the groups it contains (aspirin: acid, ester, aromatic ring; vanillin: aldehyde, phenol, ether, ring; paracetamol: amide, phenol, ring). The groups and their rough behaviour are standard textbook content.
The same group in a new molecule gives the same behaviour. An ester links the vinegar-like acid and the alcohol in a banana-smelling flavour. The amide link joins amino acids into proteins, and it is the same link that holds nylon together: a cousin in your jacket and in your muscle.
Two molecules can share a formula and be different substances. Structural isomers have their atoms connected in a different order: butane and isobutane are both C₄H₁₀. The numbers explode. There are 2 alkanes with 4 carbons, 5 with 6, 75 with 10, 366,319 with 20. That is why chemists need a system to name and draw structures.
Stereoisomers have the same connections but a different arrangement in space. The classic case is a carbon with four different groups: a stereocentre. It has two forms that are mirror images that cannot be stacked, like your hands: enantiomers. Chemically they behave identically in a symmetric world, but not inside a living cell, where enzymes and receptors are themselves handed. The two carvones smell different (R is spearmint, S is caraway), and a drug's two hands can act differently.
The thalidomide story is often told too simply. Marketed from 1957 in West Germany, thalidomide caused severe birth defects, and was withdrawn in Europe in 1961; estimates are of more than 10,000 children seriously harmed. The popular version says one mirror image cured morning sickness and the other caused the damage, so a pure sample would have been safe. In fact the two forms interconvert in the body through an acidic hydrogen on the stereocentre, so separating them would not have prevented it. The real lessons were about testing and regulation: the 1962 Kefauver-Harris Amendment in the United States and tougher drug rules in many countries. Frances Kelsey at the US FDA had held up its approval there. (This is chemistry history, not medical advice.)
Click each position to change the group on one carbon
Isomer counts for CnH2n+2 are the standard values (Wikipedia, Alkane). The maximum is 2n stereoisomers for n stereocentres; molecules with internal symmetry (meso compounds) have fewer.
Some molecules cannot be drawn correctly with one picture. Acetate (the ion left when acetic acid loses its proton) has two oxygens. One drawing puts the double bond to the first oxygen; another puts it on the second. Neither is real. The truth is a single structure in which the electrons are spread over both oxygens, and both C–O bonds are identical, in between a single and a double bond. The drawings are resonance contributors, and the real molecule, the resonance hybrid, is more stable than any of them. Benzene is the same: six carbons sharing six pi electrons, with all bonds equal.
The practical effect is acidity. A molecule is a stronger acid when its anion is more stable. The ethoxide anion from ethanol has its negative charge stuck on one oxygen. Acetate spreads it over two. Phenoxide spreads it into the ring. The result is that acetic acid (pKa 4.76) is about 10¹¹ times stronger than ethanol (15.9), with phenol (9.95) in between.
Fraction ionised = 1 / (1 + 10pKa − pH), pKa in water at 25 °C: ethanol 15.9 (Wikipedia, Ethanol), phenol 9.95 (Phenol), acetic acid 4.756 (Acid dissociation constant). Ethanol's pKa is quoted between about 15.5 and 16 in different sources.
Organic mechanisms are drawn with curly arrows, an idea usually credited to Robert Robinson in 1922. The rule is short. An arrow starts where electrons are (a lone pair or a bond) and ends where they are going (a new bond or an atom taking a lone pair). A reaction is a sequence of such arrows. It reduces memorisation to a question you can ask of any molecule: where are the electrons, and where is the electron-poor spot they would like to go to?
Take the simplest case, SN2: a nucleophile (Nu⁻, electron-rich) replaces a leaving group (X) on a carbon. One arrow goes from Nu's lone pair to carbon; another goes from the C–X bond to X. The carbon cannot hold five bonds, so the second arrow must happen as the first does. It all occurs in a single step, with Nu arriving on the side opposite X, and the carbon's three other groups flip like an umbrella in the wind. This is the Walden inversion. Because both reactants are in the one step, the rate depends on both. Hughes and Ingold, working on kinetics in the 1930s, used this signature to separate the two classic pathways and gave them the names SN1 (first order) and SN2 (second order).
Schematic: the geometry and the energy curve are idealised (an exothermic reaction with a single barrier), not computed from quantum chemistry. The H–C–X angle runs from 109.5° (tetrahedral) through 90° (planar transition state) to 70.5° (the inverted tetrahedron).
A nucleophile can also act as a base: instead of attacking the carbon, it can pluck off a hydrogen from the neighbouring carbon, pushing electrons to form a C=C bond and kicking out X. That is elimination, E2 (one step, second order) or E1 (two steps, after ionisation). Which wins? The standard rules read the carbon holding X. A methyl or primary carbon is open; SN2 can get in. A tertiary carbon is crowded, so the nucleophile cannot reach it, but it can ionise into a stable tertiary carbocation (SN1 and E1) or let a strong base pick off a hydrogen (E2). Secondary carbons sit in between, and the answer depends on the reagent. A bulky base cannot get close to the carbon but can reach the outer hydrogens, so it eliminates. Heat favours elimination, because it makes more molecules. Polar protic solvents help the ionising paths; polar aprotic ones help SN2.
Substrate
Reagent
Temperature
A lookup of the textbook decision rules (e.g. Clayden et al., Organic Chemistry), for understanding which factor matters, not a prediction tool for real syntheses. Examples of the reagent types are given in the labels.
An alkene's pi bond is a rich, exposed cloud of electrons sitting above and below the plane, easy to reach. So alkenes act as nucleophiles and react with electrophiles: acids, bromine. In the addition of H–Br to an alkene, the pi electrons attack the hydrogen (curly arrow 1), H–Br breaks (arrow 2), and a carbocation forms on the carbon that did not get the hydrogen. Then bromide attacks the cation (arrow 3).
The hydrogen can land on either carbon of an unsymmetrical alkene, and the choice decides the product. It goes where it leaves the more stable cation, and a cation is more stable the more alkyl groups are attached to its carbon, since they donate electrons toward its empty orbital (hyperconjugation and induction). Tertiary beats secondary beats primary. This is Markovnikov's rule, formulated by Vladimir Markovnikov around 1870 from observations, and explained by the cation a century later. It is an example of the series' big idea: reactions go where the intermediate is most stable.
Primary, secondary and tertiary refer to the number of alkyl groups on the cationic carbon (1, 2, 3). Stability order tertiary > secondary > primary is the textbook result. Under the conditions assumed here (no peroxides).
Organic chemistry is shape, groups and electrons. Carbon's hybrids set the shape; a few functional groups set the behaviour; and curly arrows track electrons from rich spots to poor ones. When a reaction has a choice, it goes through the more stable intermediate, the less crowded path, or the lower barrier.
Try this: this week, read the ingredient list on a food or medicine package and pick one name ending in -ate, -ol or -amine. Say which functional group it names and what that group tends to do. (Nothing to mix or heat; a pen is enough.)
Sources. Hybridisation, functional groups, resonance, SN1/SN2/E1/E2 and Markovnikov are standard textbook organic chemistry (Clayden et al.; OpenStax Organic Chemistry). van 't Hoff's 1874 pamphlet on tetrahedral carbon (Wikipedia, Jacobus Henricus van 't Hoff). Kekulé's benzene paper, 1865 (Wikipedia, Benzene). Curly arrows by Robert Robinson, 1922 (Wikipedia, Arrow pushing). Hughes and Ingold kinetic work, 1937 (Wikipedia, SN2 reaction). Carvone: R is spearmint, S is caraway (Wikipedia, Carvone). Thalidomide: marketed 1957 in West Germany, withdrawn in Europe 1961, over 10,000 children severely harmed, enantiomers interconvert in the body (Wikipedia, Thalidomide). Alkane isomer counts (Wikipedia, Alkane). Bertozzi, Meldal and Sharpless, Nobel Prize in Chemistry 2022. Mechanisms only; no procedures. Go deeper.