Glossary
Alphabetical reference of recurring terminology and conventions used throughout this guide. Terms are added the first time they’re formally introduced in the text and checked for consistent usage (spelling, capitalization, phrasing) in later chapters.
Terms
Acetal — A carbon bonded to two alkoxy (–OR) groups, formed when a hemiacetal reacts with a second equivalent of alcohol; important in carbohydrate chemistry. (Part V Ch. 12, Carbonyl Compounds and Nucleophilic Addition)
Acid chloride — A carboxylic acid derivative with Cl in place of OH (–C(=O)Cl); the most reactive of the common carbonyl derivatives toward nucleophilic acyl substitution. (Part V Ch. 13, Carboxylic Acids and Their Derivatives)
Activating / deactivating group — A ring substituent that increases (activating) or decreases (deactivating) an aromatic ring’s reactivity toward electrophiles by donating or withdrawing electron density via resonance or induction. (Part VI Ch. 17, Substituent Effects and Aromatic Compounds)
Acylium ion — A resonance-stabilized R–C≡O⁺ cation, the electrophile generated in Friedel-Crafts acylation. (Appendix C, Reaction Summary Tables)
Alcohol — A compound containing an O–H group bonded to a saturated carbon; capable of hydrogen bonding. (Part III Ch. 1, Functional Groups)
Aldehyde — A carbonyl compound with the C=O group at the end of a carbon chain, bonded to at least one hydrogen; reactive toward nucleophiles. (Part III Ch. 1, Functional Groups)
Aldol reaction — The addition of an enolate to a carbonyl compound, forming a new carbon-carbon bond and a β-hydroxy carbonyl product. (Part V Ch. 14, Enols, Enolates, and Carbon-Carbon Bond Formation)
Alkane — A hydrocarbon containing only single bonds; generally nonpolar and relatively unreactive. (Part III Ch. 1, Functional Groups)
Alkene — A hydrocarbon containing at least one carbon-carbon double bond. (Part III Ch. 1, Functional Groups)
Alkyl halide — A compound with a halogen (F, Cl, Br, I) bonded to an sp³ carbon; the halogen is a good leaving group, making these the classic substrate for substitution and elimination. (Appendix A, Functional Group Atlas; first used Part IV Ch. 7)
Alkyne — A hydrocarbon containing at least one carbon-carbon triple bond. (Part III Ch. 1, Functional Groups)
Allylic — Describes a position adjacent to a carbon-carbon double bond; allylic carbocations and radicals are resonance-stabilized. (Part III Ch. 2, Resonance)
Alpha (α) proton / position — A hydrogen (or carbon) directly adjacent to a carbonyl group; alpha protons are unusually acidic because their removal produces a resonance-stabilized enolate. (Part V Ch. 14, Enols, Enolates, and Carbon-Carbon Bond Formation)
Amide — A compound containing a carbonyl bonded to a nitrogen (–C(=O)–N–); forms the peptide bond in proteins. (Part III Ch. 1, Functional Groups)
Amine — An organic base containing nitrogen. (Part III Ch. 1, Functional Groups)
Anhydride — A carboxylic acid derivative formed from two acyl groups joined by an oxygen (–C(=O)–O–C(=O)–); more reactive than esters or amides toward nucleophilic acyl substitution. (Part V Ch. 13, Carboxylic Acids and Their Derivatives)
Anti-periplanar — A geometry in which two groups (the leaving group and the departing hydrogen in E2) are positioned on opposite sides of the molecule in the same plane; required for E2 elimination. (Part IV Ch. 8, Elimination Reactions)
Arene — An aromatic ring system (e.g., benzene); resists addition and undergoes electrophilic aromatic substitution instead. (Appendix A, Functional Group Atlas)
Aromaticity — The unusual stability of certain cyclic, planar, fully conjugated systems (like benzene) arising from complete electron delocalization; requires satisfying Hückel’s rule. (Part VI Ch. 15, Benzene and Aromaticity)
ARIO — A mnemonic for ranking acid strength by conjugate-base stability: Atom (electronegativity/size), Resonance, Induction, Orbital (hybridization). (Part III Ch. 3, Acids and Bases)
Axial — A substituent position on a cyclohexane chair that points perpendicular to the ring’s average plane, alternating up and down around the ring. (Part III Ch. 4, Stereochemistry)
Brønsted-Lowry acid/base — An acid is a proton donor; a base is a proton acceptor. The definition organic chemistry uses almost exclusively. (Part II, Acids and Bases)
Cahn-Ingold-Prelog (CIP) rules — The priority system (by atomic number, then outward along the chain) used to rank substituents for both R/S stereocenter and E/Z double-bond nomenclature. (Appendix E, IUPAC Nomenclature Reference)
Carbanion — A carbon bearing a negative charge and a lone pair, typically with three bonds. (Part IV Ch. 6, Introduction to Mechanisms)
Carbocation — A carbon bearing a positive charge and only three bonds; stability increases with resonance delocalization and alkyl substitution. (Part III Ch. 2, Resonance)
Carboxylic acid — A compound containing both a carbonyl and a hydroxyl group on the same carbon (–COOH); relatively acidic. (Part III Ch. 1, Functional Groups)
Chair conformation — The lowest-energy three-dimensional shape of cyclohexane, in which every bond angle is near 109.5° and every neighboring pair of hydrogens is staggered. (Part III Ch. 4, Stereochemistry)
Chemical shift — The position (in ppm) at which a nucleus resonates in an NMR spectrum, reflecting its electronic environment (shielding/deshielding). (Part VII Ch. 19, Nuclear Magnetic Resonance Spectroscopy)
Chirality — The property of an object (or molecule) that is not superimposable on its mirror image. (Part III Ch. 4, Stereochemistry)
Claisen condensation — The reaction of an ester enolate with another ester, forming a new carbon-carbon bond and a β-keto ester product. (Part V Ch. 14, Enols, Enolates, and Carbon-Carbon Bond Formation)
Conformation — A three-dimensional shape a molecule adopts through bond rotation, without breaking any bonds; conformations interconvert freely and are distinct from configurations. (Part III Ch. 4, Stereochemistry)
Conjugate acid / conjugate base — The species formed when an acid loses a proton (conjugate base) or a base gains one (conjugate acid). (Part II, Acids and Bases)
Conjugation — An arrangement of alternating multiple and single bonds (or a lone pair/charge adjacent to a π bond) that allows electron delocalization. (Part III Ch. 2, Resonance)
Coupling constant (J) — The frequency spacing (in Hz) between split peaks in an NMR signal, reflecting the geometric relationship between coupled protons (e.g., larger for trans-alkene protons than cis). (Appendix D, Spectroscopy Reference)
Curved arrow — The notation organic chemists use to show electron movement (not atom movement) during a reaction. (Part III Ch. 5, Electron Flow)
Delocalization — The spreading of electron density over multiple atoms rather than concentrating it on one, which generally increases stability. (Part III Ch. 2, Resonance)
Diastereomer — A stereoisomer that is not a mirror image of another stereoisomer. (Part III Ch. 4, Stereochemistry)
Diaxial interaction (1,3-) — Steric strain between an axial substituent and the axial hydrogens two carbons away on the same face of a cyclohexane chair; grows with substituent size and disfavors the axial position. (Part III Ch. 4, Stereochemistry)
Electronegativity — An atom’s tendency to attract shared electrons in a bond; increases across a period and up a group. (Part II, Atomic Structure and Periodic Trends)
Electrophile — An electron-poor atom or molecule that accepts an electron pair to form a new bond (e.g., carbocations, positively charged or polarized species). (Part III Ch. 5, Electron Flow)
Electrophilic aromatic substitution (EAS) — The reaction pattern by which aromatic rings react: an electrophile attacks the ring, aromaticity is temporarily lost, then restored by loss of a proton; includes halogenation, nitration, sulfonation, and Friedel-Crafts reactions. (Part VI Ch. 16, Electrophilic Aromatic Substitution)
E/Z nomenclature — The unambiguous system for naming double-bond geometry: Z (zusammen) means the two higher-priority groups are on the same side, E (entgegen) means opposite sides; priority assigned by CIP rules. (Appendix E, IUPAC Nomenclature Reference)
E1 / E2 — The two dominant elimination mechanisms: E2 is a one-step, concerted removal of a proton and a leaving group requiring anti-periplanar geometry, favored by strong bases; E1 is a two-step mechanism proceeding through a carbocation intermediate (shares substrate/solvent preferences with SN1), favored by weak bases and prone to rearrangement. (Part IV Ch. 8, Elimination Reactions)
Enantiomer — A mirror-image stereoisomer of a chiral molecule. (Part III Ch. 4, Stereochemistry)
Enol / Enolate — A tautomer of a carbonyl compound with a C=C–OH group (enol), or its deprotonated, resonance-stabilized conjugate base (enolate) formed by removing an alpha proton; enolates act as powerful nucleophiles. (Part V Ch. 14, Enols, Enolates, and Carbon-Carbon Bond Formation)
Equatorial — A substituent position on a cyclohexane chair that points roughly in the plane of the ring, outward; generally preferred over axial for larger substituents. (Part III Ch. 4, Stereochemistry)
Equilibrium constant (Ka) — A numerical measure of the position of equilibrium for a reversible reaction; for acids, related to pKa by pKa = −log(Ka). (Part II, Equilibrium)
Ester — A compound containing a carbonyl bonded to an alkoxy group (–C(=O)–O–); common in fats and lipids. (Part III Ch. 1, Functional Groups)
Ether — A compound containing an oxygen atom bonded between two carbon groups; less reactive than alcohols. (Part III Ch. 1, Functional Groups)
Formal charge — The charge an atom would have if bonding electrons were shared equally; calculated from valence electrons, lone pair electrons, and bonds. (Part II, Lewis Structures)
Fragmentation — The breaking apart of a molecular ion into smaller charged and neutral pieces inside a mass spectrometer, producing a pattern of peaks that helps reveal structure. (Part VII Ch. 20, Mass Spectrometry and Structure Determination)
Friedel-Crafts reaction — An electrophilic aromatic substitution that forms a new carbon-carbon bond to the ring (alkylation or acylation). (Part VI Ch. 16, Electrophilic Aromatic Substitution)
Functional group — A recurring arrangement of atoms that determines a molecule’s characteristic physical and chemical behavior. (Part III Ch. 1, Functional Groups)
Halonium ion — A bridged, three-membered cyclic cation formed when X₂ adds to an alkene; forces the second halogen to attack from the opposite face, giving anti addition. (Appendix C, Reaction Summary Tables)
Hemiacetal — A carbon bonded to both an –OH and an –OR group, formed by addition of one equivalent of alcohol to a carbonyl; an intermediate on the way to an acetal. (Part V Ch. 12, Carbonyl Compounds and Nucleophilic Addition)
Heterocycle — A cyclic compound containing at least one ring atom other than carbon, most often nitrogen, oxygen, or sulfur. (Part VI Ch. 17, Substituent Effects and Aromatic Compounds)
Hückel’s rule — A cyclic, planar, fully conjugated system is aromatic when it contains 4n+2 π electrons, where n is a whole number (2, 6, 10, 14, and so on). (Part VI Ch. 15, Benzene and Aromaticity)
Hybridization (sp³, sp², sp) — The mixing of atomic orbitals that determines a carbon’s geometry: sp³ is tetrahedral, sp² is trigonal planar, sp is linear. (Part II, Hybridization)
Inductive effect — The stabilizing or destabilizing pull on electron density through sigma bonds caused by a nearby electronegative atom or electron-withdrawing group. (Part III Ch. 3, Acids and Bases)
Infrared (IR) spectroscopy — A technique that identifies functional groups from characteristic bond-vibration absorptions, typically reported by wavenumber. (Part VII Ch. 18, Infrared Spectroscopy and Functional Group Identification)
Integration (NMR) — The relative area under an NMR signal, proportional to the number of equivalent nuclei producing it. (Part VII Ch. 19, Nuclear Magnetic Resonance Spectroscopy)
Intermediate — A temporary, often unstable species (e.g., a carbocation, carbanion, or radical) formed partway through a reaction mechanism before the final product. (Part IV Ch. 6, Introduction to Mechanisms)
Inversion (Walden inversion) — The flip in stereochemical configuration at a reaction center, characteristic of SN2 backside attack. (Part IV Ch. 7, Substitution Reactions)
Hyperconjugation — The stabilizing donation of electron density from an adjacent sigma bond (e.g., C–H) into an empty or partially empty orbital, such as a carbocation or an aromatic ring. (Part VI Ch. 17, Substituent Effects and Aromatic Compounds)
IUPAC nomenclature — The systematic naming system built from a parent chain (longest continuous carbon chain), a suffix (signaling the principal functional group), and prefixes/locants (identifying substituents and their positions). (Part III Ch. 1, Functional Groups)
Keto-enol tautomerism — The equilibrium between a carbonyl compound (keto form) and its enol form, which differ in the position of a proton and a double bond; the keto form is usually favored. (Part V Ch. 14, Enols, Enolates, and Carbon-Carbon Bond Formation)
Ketone — A carbonyl compound with the C=O group bonded to two carbons within a chain (not terminal). (Part III Ch. 1, Functional Groups)
LDA (lithium diisopropylamide) — A strong, sterically hindered, non-nucleophilic base used to cleanly deprotonate a carbonyl’s alpha-carbon to form an enolate without competing as a nucleophile. (Appendix C, Reaction Summary Tables)
Le Châtelier’s principle — A system at equilibrium shifts in a predictable direction in response to a change in reactant/product concentration, temperature, or pressure. (Part II, Equilibrium)
Leaving group — An atom or group of atoms that departs from a molecule during a reaction, taking a bonding pair of electrons with it; better leaving groups stabilize that negative charge more effectively. (Part IV Ch. 6, Introduction to Mechanisms)
Lewis structure — A diagram showing an atom’s or molecule’s valence electrons as bonds and lone pairs. (Part II, Lewis Structures)
Locant — A number or descriptor (e.g., R/S) identifying the position of a substituent or stereocenter on a parent chain. (Part III Ch. 1, Functional Groups)
Markovnikov’s rule — In addition of HX (or similar) to an unsymmetrical alkene, the electrophile adds to give the more stable (more substituted) carbocation intermediate, predicting the major product. (Part IV Ch. 9, Addition Reactions)
Mass spectrometry — A technique that ionizes and fragments a molecule to reveal its molecular weight, isotopic pattern, and characteristic fragment losses. (Part VII Ch. 20, Mass Spectrometry and Structure Determination)
Meta director — A ring substituent (typically electron-withdrawing with a positive or partial-positive atom adjacent to the ring) that directs electrophilic aromatic substitution to the meta position, avoiding destabilizing charge buildup at ortho/para. (Part VI Ch. 17, Substituent Effects and Aromatic Compounds)
Molecular ion (M⁺) — The peak in a mass spectrum corresponding to the intact, ionized starting molecule, before fragmentation; its mass gives the molecular weight. (Part VII Ch. 20, Mass Spectrometry and Structure Determination)
n+1 rule — In ¹H NMR, a proton with n chemically non-equivalent neighboring protons is split into n+1 peaks. (Appendix D, Spectroscopy Reference; first introduced Part VII Ch. 19)
Nuclear magnetic resonance (NMR) spectroscopy — A technique that reveals molecular structure from the chemical shift, integration, and splitting pattern of individual atomic environments (commonly ¹H and ¹³C). (Part VII Ch. 19, Nuclear Magnetic Resonance Spectroscopy)
Nucleophile — An electron-rich atom or molecule that donates an electron pair to form a new bond (e.g., hydroxide, water, ammonia). (Part III Ch. 5, Electron Flow; first mentioned Part II, Molecular Geometry)
Nucleophilic acyl substitution — The mechanism by which carboxylic acid derivatives react: nucleophilic attack at the carbonyl carbon, formation of a tetrahedral intermediate, then departure of a leaving group restores the carbonyl. Relative reactivity follows leaving-group ability: acid chlorides > anhydrides > esters > amides. (Part V Ch. 13, Carboxylic Acids and Their Derivatives)
Ortho/para director — A ring substituent that directs electrophilic aromatic substitution to the ortho and para positions, typically by donating electron density (by resonance or, for halogens, despite net-withdrawing induction) into those positions. (Part VI Ch. 17, Substituent Effects and Aromatic Compounds)
pKa — The negative log of the acid dissociation constant (Ka); lower pKa indicates a stronger acid. (Part II, Acids and Bases)
pKaH — The pKa of a base’s conjugate acid, used to report basicity indirectly; a higher pKaH means a stronger base. (Appendix B, pKa Tables)
Pi (π) bond — A bond formed from side-on overlap of unhybridized p orbitals; found in double and triple bonds and more reactive than sigma bonds. (Part II, Chemical Bonding)
Polar protic / polar aprotic solvent — Protic solvents (e.g., water, alcohols) have an O–H or N–H bond and favor SN1 by stabilizing cations and leaving groups through hydrogen bonding; aprotic solvents (e.g., acetone, DMSO) lack that bond and favor SN2 by leaving the nucleophile more reactive. (Part IV Ch. 7, Substitution Reactions)
Protecting group — A group temporarily added to block one reactive site on a molecule so a reaction can be carried out selectively elsewhere, then removed afterward. (Part VIII Ch. 22, Named Reactions and Protecting Groups)
Racemization — The formation of a racemic (1:1 enantiomer) mixture, typical of SN1 reactions where a planar carbocation intermediate is attacked from either face. (Part IV Ch. 7, Substitution Reactions)
Radical — A species with an unpaired electron, formed when a bond breaks homolytically. (Part IV Ch. 6, Introduction to Mechanisms)
Regiochemistry — The question of which position on a molecule a reaction occurs at, distinct from stereochemistry (which spatial arrangement results) and connectivity (which atoms are bonded). (Part IV Ch. 9, Addition Reactions)
Resonance — The use of multiple valid Lewis structures (“resonance structures” or “contributors”) that differ only in electron placement to represent a single molecule’s true electron distribution (the “resonance hybrid”); delocalization generally increases stability. (Part III Ch. 2, Resonance; first mentioned Part II, Medium Priority)
Retrosynthesis — A planning strategy that works backward from a target molecule, breaking it into simpler precursors by asking “how might this be constructed?” rather than “what would this produce?” (Part VIII Ch. 21, Retrosynthesis and Multi-Step Synthesis)
Ring flip — The interconversion of one cyclohexane chair into another via bond rotation, which swaps every axial position for equatorial (and vice versa) without breaking bonds or changing configuration. (Part III Ch. 4, Stereochemistry)
Shielding / deshielding — The degree to which nearby electron density shields (upfield shift) or exposes (downfield/deshielded shift) a nucleus from an applied magnetic field, determining its chemical shift. (Part VII Ch. 19, Nuclear Magnetic Resonance Spectroscopy)
Sigma (σ) bond — A bond formed from head-on orbital overlap; forms the single-bond backbone of every organic molecule. (Part II, Chemical Bonding)
SN1 / SN2 — The two dominant substitution mechanisms: SN2 is a one-step, concerted backside attack favored by strong nucleophiles and unhindered substrates (inversion of configuration); SN1 is a two-step mechanism proceeding through a carbocation intermediate, favored by stable cations and polar protic solvents (racemization). (Part IV Ch. 7, Substitution Reactions)
Splitting pattern — The division of an NMR signal into multiple peaks caused by coupling with neighboring, non-equivalent hydrogens. (Part VII Ch. 19, Nuclear Magnetic Resonance Spectroscopy)
Stereocenter — An atom (usually carbon) whose four different substituents give it two non-superimposable spatial arrangements, described by R/S configuration. (Part III Ch. 4, Stereochemistry)
Steric effects (steric strain) — Repulsive interactions between atoms or groups in close spatial proximity that raise energy and disfavor certain conformations, geometries, or reaction pathways. (Part IV Overview, Mechanistic Thinking)
Tetrahedral intermediate — The sp³ carbon species formed when a nucleophile adds to a carbonyl carbon, before a leaving group departs (in substitution) or a proton transfer restores neutrality (in addition). (Part V Ch. 13, Carboxylic Acids and Their Derivatives)
Valence electrons — The electrons in an atom’s outermost shell, responsible for bonding. (Part II, Atomic Structure and Periodic Trends)
VSEPR theory — Valence Shell Electron Pair Repulsion; predicts molecular geometry from the number of bonding and lone electron pairs around a central atom. (Part II, Molecular Geometry)
Wavenumber — The unit (cm⁻¹) used to report absorption position in an IR spectrum; proportional to vibrational frequency. (Part VII Ch. 18, Infrared Spectroscopy and Functional Group Identification)
Zaitsev product — The more substituted (generally more stable) alkene formed as the major product of an elimination reaction, favored except when a bulky base is used. (Appendix C, Reaction Summary Tables)
Written and maintained by Patrick Carrington.