Organic chemistry

Organic chemistry studies carbon-based molecular structures and their transformations, with emphasis on connectivity, functional groups, and stereochemistry. Carbon's ability to form chains, rings, and multiple bonds supports a very large range of molecular architectures.

A reaction can change one functional group while preserving the rest of a framework, or form a new carbon-carbon bond that enlarges it. Following electron movement and testing competing mechanisms makes these transformations predictable rather than a catalogue of isolated recipes.

A molecule belonging to organic chemistry; its presence alone is not evidence of life.

Material containing organic molecules, whether produced by life or by abiotic processes.

Acid-promoted union of a carbonyl-derived oxocarbenium ion with a tethered alkene to form a ring. Cation trapping and the preferred cyclization conformation determine the final substitution and stereochemistry.

An energetic penalty from bond angles, torsions or nonbonded contacts forced away from favourable values by ring closure.

Torsional strain is an increase in the energy of a molecule associated with an unfavourable torsion angle, relative to a stated reference conformation. Rotation about a bond can change the relative orientations of substituents without changing which atoms are bonded. The IUPAC definition of strain explicitly includes unfavourable dihedral angles alongside bond-length and bond-angle distortions.^[ref]

Consider ethane viewed along its central carbon–carbon bond. An eclipsed conformation aligns projected carbon–hydrogen bonds, whereas a staggered conformation places them between one another. An idealized threefold potential energy model iswith $\varphi =0$ chosen eclipsed. It gives $V(0)=V_3$ and $V(\pi /3)=0$: a finite rotational barrier separates equivalent minima. The model is a teaching parametrization; $V_3$ must be obtained independently rather than read from the drawing.

The 1937 paper by J. D. Kemp and K. S. Pitzer explicitly connected the entropy of ethane and the third law of thermodynamics with hindered methyl-group rotation.^[ref] This historical connection shows why internal rotation is a measurable molecular degree of freedom, not simply unrestricted motion around a single bond. In a ring, geometric closure can restrict accessible torsion angles; ring strain can therefore include torsional strain as well as other contributions. Assigning a separate torsional energy is model-dependent, rather than a complete account of every electronic interaction.

Construction of organic compounds through controlled transformations of simpler precursors.

A total synthesis constructs a target compound from simpler starting materials through a planned sequence of chemical reactions. For a complex target, success includes the required connectivity and stereochemistry, not merely the elemental formula or an approximate mass.

Tropinone provides a classic strategic example: compatible small precursors can assemble a bridged framework through a coordinated sequence, rather than making every ring separately.^[ref] A route's value also depends on selectivity, yield, operational reliability and how easily structural identity can be established. “Total” does not require that every carbon atom begin as an element.

Working backward from a target to identify bonds, functional-group changes and simpler precursors that correspond to plausible forward reactions. Tracking atoms and stereochemistry tests a proposed disconnection.

Assigning the origin and destination of atoms through a synthetic route. carbon counts and the positions of surviving carbonyls expose chain-length and ring-connectivity errors.

A mechanistic correlation by which different reactant stereoisomers lead to different product stereoisomers.

An atom at which exchange of two substituents produces a stereoisomer. A tetrahedral carbon with four distinct substituents is a familiar example.

A carbon bearing both a hydroxyl group and an amino substituent, commonly formed by amine addition to a carbonyl. Cyclic hemiaminals can equilibrate with open-chain carbonyl compounds.

A species with a neutral divalent carbon bearing two nonbonding electrons. Singlet and triplet states differ in their bonding and reaction pathways.

An alkylidene complex with substantial nucleophilic/dianionic carbene character, commonly involving an early high-oxidation-state metal and strongly donating ancillary ligands.

A metal carbene with substantial electrophilic character at carbon, commonly stabilized by a heteroatom substituent and attached to a low-oxidation-state metal carrying pi-acceptor ligands.

A carbene centre in a nitrogen-containing heterocycle, often used as a strong sigma-donor ligand. Steric substitution on nitrogen controls access to a coordinated metal.

A species that transfers carbene-like bonding reactivity without requiring an isolated free carbene. Its reaction depends on its metal or other associated group as well as its substituents.

A metal-associated carbene-like reactive centre. Loss of nitrogen from a diazo precursor can generate a centre capable of alkene cyclopropanation; the catalyst and substituents influence its selectivity.

An alkene with two oxygen substituents on one alkene carbon. Allylic ketene acetals rearrange to unsaturated esters.

A ketene conjugated with a nonaromatic quinoid ring. Elimination from suitable para-hydroxybenzoate anions can form a transient exocyclic ketene that is trapped by water.

Interaction of a filled sigma bond with a neighboring empty or partially occupied orbital. Orbital alignment controls its stabilizing influence and secondary isotope effects.

Elimination through a conjugate base formed before leaving-group departure. The measured kinetic order depends on whether deprotonation equilibrates and which step limits the rate.

Intramolecular electrophilic aromatic substitution that closes a carbon ring. Tether geometry and arene substitution control the accessible site and stereochemistry.

A five-atom pericyclic rearrangement that shifts a sigma bond across adjacent two- and three-atom fragments. Allylic ammonium ylides transfer the terminal allyl carbon to the ylide carbon.

A neutral species with adjacent formally positive and negative centres. Ammonium ylides can undergo stereospecific [2,3]-sigmatropic rearrangements.

A charge-separated species with a nucleophilic carbon adjacent to positively charged sulfur. Conjugate addition followed by displacement of a sulfur leaving group can produce carbocycles or heterocycles.

A ylide with adjacent phosphorus-positive and carbon-negative descriptions, often represented by a phosphorane form. Its carbon can be coupled to a carbonyl carbon in Wittig olefination.

Conjugate addition of a nitrogen nucleophile to an electron-poor alkene. Intramolecular addition can close a nitrogen-containing ring.

Olefination of a carbonyl compound by a stabilized phosphonate carbanion, with phosphate elimination. Many common conditions favor an E alkene.

Carbene addition to an aromatic bond gives a cyclopropane-containing intermediate that can open to a seven-membered cycloheptatriene.

A carbonyl compound with two imidazolyl leaving groups. It activates carboxylic acids as acyl imidazoles, releasing carbon dioxide and imidazole.

A concerted six-electron [3,3]-sigmatropic rearrangement of an allyl vinyl ether into an unsaturated carbonyl compound. Suprafacial bond reorganization correlates stereochemistry across the allyl fragment.

An allylic ester is converted to a silyl ketene acetal, which undergoes a [3,3]-sigmatropic rearrangement to an unsaturated carboxylic-acid derivative.

An allylic alcohol reacts with an orthoester under weak-acid catalysis to give a ketene acetal, which rearranges to an unsaturated ester.

Oxidative conversion of a furfuryl alcohol into a six-membered oxygen heterocycle, often a hydroxypyranone. Oxidation, furan opening and intramolecular lactol formation explain the ring expansion.

A cluster of lithium atoms and carbon-containing ligands in an organolithium solution. Aggregation and exchange depend on solvent, concentration and additional salts.

Catalytic redistribution of carbon–carbon double-bond partners. Intramolecular and intermolecular reactions can compete, producing rings, chains and small alkene coproducts.

A four-membered ring containing one metal and three carbon atoms. Its formation and alternate fragmentation exchange alkylidene groups during olefin metathesis.

Step-growth polymerization in which terminal diene groups undergo intermolecular olefin metathesis. Removing a volatile alkene coproduct can drive conversion.

Intramolecular olefin metathesis connecting two alkene sites into a ring. Terminal-alkene substrates can release ethene; concentration and preorganization influence competition with chain growth.

A compound containing a carbon–nitrogen double bond. Reversible condensation of an aldehyde with a primary amine gives an imine and water under suitable conditions.

An imine whose imine carbon bears two carbon substituents. Hydrolysis passes through a carbinolamine and gives a ketone.

A protecting group temporarily changes a reactive functional group so that another transformation can proceed selectively. It is installed, survives the desired intervening conditions, and is later removed to regenerate the functionality.

For example, converting an alcohol into a suitable protected derivative can suppress its reaction during a different bond-forming step. Protection is useful only if the installation and removal are sufficiently selective; a group stable under one set of conditions can be unsuitable under another.

Cleavage of a silicon–oxygen protecting group to reveal an alcohol. Fluoride can drive the transformation through strong silicon–fluorine bond formation.

A cyclic acetal protecting group made from an alcohol and dihydropyran. It protects the original alcohol oxygen and can be removed under suitable acidic hydrolysis conditions.

A tert-butoxycarbonyl group used to protect an amine as a carbamate. Acid-promoted cleavage releases carbon dioxide and restores the amine.

A functional group that can later be converted into a carbonyl at a mapped carbon. A secondary nitro group is a useful example when it also enables carbon–carbon bond formation before unmasking.

Use of ester protecting groups that can be selectively removed under different conditions. A methyl/tert-butyl pair can permit kinetic base hydrolysis at one end and acid-promoted alkyl cleavage at the other.