Appendix C | Glossary

Kirsten Kramer; Cassandra Lilly

Appendix C | Glossary

Absolute configuration (Section 3.5): The exact three-dimensional structure of a chiral molecule. Absolute configurations are specified verbally by the Cahn–Ingold– Prelog R,S convention.
Acetals, R₂C(OR′)₂ (Section 10.9): A type of functional group consisting of two −OR groups bonded to the same carbon, R₂C(OR′)₂. Acetals are often used as protecting groups for ketones and aldehydes.

Acetyl group (Section 10.1): The CH₃CO^– group.
Acetylide anion (Section 5.13): The anion formed by removal of a proton from a terminal alkyne, R–C≡C:^–.
Achiral (Section 3.2): Having a lack of handedness. A molecule is achiral if it has a plane of symmetry and is thus superimposable on its mirror image.
Acid anhydrides (Chapter 11 Introduction): A type of functional group with two acyl groups bonded to a common oxygen atom, RCO₂COR′.
Acid halides (Chapter 11 Introduction): A type of functional group with an acyl group bonded to a halogen atom, RCOX.
Acidity constant, K_a (Section 1.18): A measure of acid strength. For any acid HA, the acidity constant is given by the expression:
- 𝐾_a = [H₃O⁺][A^–]/[HA]
Activating groups (Section 5.5): Electron-donating groups such as hydroxyl (−OH) or amino (−NH₂) that increase the reactivity of an aromatic ring toward electrophilic aromatic substitution.
Activation energy (Section 4.8): The difference in energy between ground state and transition state in a reaction. The amount of activation energy determines the rate at which the reaction proceeds. Most organic reactions have activation energies of 40– 100 kJ/mol.
Acyl group (Section 8.5, Section 10.1): A −COR group.
Acyl phosphates (Chapter 11 Introduction): A type of functional group with an acyl group bonded to a phosphate, RCO₂PO₃²⁻.
Acylation (Section 8.5, Section 12.5): The introduction of an acyl group, −COR, onto a molecule. For example, acylation of an alcohol yields an ester, acylation of an amine yields an amide, and acylation of an aromatic ring yields an alkyl aryl ketone.
Acylium ion (Section 8.5): A resonance-stabilized carbocation in which the positive charge is located at a carbonyl-group carbon, R–C═O ↔ R–C≡O ions are intermediates in Friedel–Crafts acylation reactions.
1,2-Addition (Section 5.9): Addition of a reactant to the two ends of a double bond.
1,4-Addition (Section 5.9): Addition of a reactant to the ends of a conjugated π system. Conjugated dienes yield 1,4 adducts when treated with electrophiles such as HCl. Conjugated enones yield 1,4 adducts when treated with nucleophiles such as amines.
Addition reactions (Section 4.5): Occur when two reactants add together to form a single product with no atoms left over.
Alcohols (Section 2.1, Chapter 9 Introduction): A class of compounds with an −OH group bonded to a saturated, sp³-hybridized carbon, ROH.
Aldehydes (RCHO) (Section 3.1, Chapter 19 Introduction): A class of compounds containing the −CHO functional group.
Alicyclic (Section 2.5): A nonaromatic cyclic hydrocarbon such as a cycloalkane or cycloalkene.
Aliphatic (Section 2.2): A nonaromatic hydrocarbon such as a simple alkane, alkene, or alkyne.
Alkaloids (Chapter 1 Chemistry Matters): Naturally occurring organic bases, such as morphine.
Alkanes (Section 2.2): A class of compounds of carbon and hydrogen that contains only single bonds.
Alkene (Section 2.1): A hydrocarbon that contains a carbon–carbon double bond, R₂C═CR₂.
Alkoxide ion, RO⁻ (Section 9.2): The anion formed by deprotonation of an alcohol.
Alkoxymercuration (Section 9.11): A method for synthesizing ethers by mercuric- ion catalyzed addition of an alcohol to an alkene followed by demercuration on treatment with NaBH₄.
Alkyl group (Section 2.3): The partial structure that remains when a hydrogen atom is removed from an alkane.
Alkyl halide (Section 2.1, Chapter 6 Introduction): A compound with a halogen atom bonded to a saturated, sp³-hybridized carbon atom.
Alkylamines (Section 12.1): Amino-substituted alkanes RNH₂, R₂NH, or R₃N.
Alkylation (Section 5.14, Section 8.5, Section 9.11): Introduction of an alkyl group onto a molecule. For example, aromatic rings can be alkylated to yield arenes, and enolate anions can be alkylated to yield α-substituted carbonyl compounds.
Alkyne (Section 2.1, Chapter 5 Introduction): A hydrocarbon that contains a carbon–carbon triple bond, RC≡CR.
Allyl group (Section 4.1): A H₂C═CH(CH₃)- substituent.
Allylic (Section 6.3): The position next to a double bond. For example, H₂C═CHCH₂Br is an allylic bromide.
Amides (Section 2.1, Chapter 12 Introduction): A class of compounds containing the −CONR₂ functional group.
Amines (Section 2.1): A class of compounds containing one or more organic substituents bonded to a nitrogen atom, RNH₂, R₂NH, or R₃N.
Angle strain (Section 2.10): The strain introduced into a molecule when a bond angle is deformed from its ideal value. Angle strain is particularly important in small-ring cycloalkanes, where it results from compression of bond angles to less than their ideal tetrahedral values.
Anti conformation (Section 2.8): The geometric arrangement around a carbon– carbon single bond in which the two largest substituents are 180° apart as viewed in a Newman projection.
Anti periplanar (Section 7.8): Describing the stereochemical relationship in which two bonds on adjacent carbons lie in the same plane at an angle of 180°.
Anti stereochemistry (Section 5.4): The opposite of syn. An anti addition reaction is one in which the two ends of the double bond are attacked from different sides. An anti elimination reaction is one in which the two groups leave from opposite sides of the molecule.
Antibonding MO (Section 1.11): A molecular orbital that is higher in energy than the atomic orbitals from which it is formed..
Arene (Section 8.2): An alkyl-substituted benzene.
Aromaticity (Chapter 8 Introduction): The special characteristics of cyclic conjugated molecules, including unusual stability and a tendency to undergo substitution reactions rather than addition reactions on treatment with electrophiles. Aromatic molecules are planar, cyclic, conjugated species with 4n + 2 π electrons.
Arylamines (Section 12.1): Amino-substituted aromatic compounds, ArNH₂.
Atomic mass (Section 1.1): The weighted average mass of an element’s naturally occurring isotopes.
Atomic number, Z (Section 1.1): The number of protons in the nucleus of an atom.
Aufbau principle (Section 1.3): The rules for determining the electron configuration of an atom.
Axial bonds (Section 2.13): Bonds or positions in chair cyclohexane that lie along the ring axis, perpendicular to the rough plane of the ring.
Azide synthesis (Section 12.4): A method for preparing amines by S_N2 reaction of an alkyl halide with azide ion, followed by reduction.

Basicity constant, K_b(Section 12.3): A measure of base strength in water. For any base B, the basicity constant is given by the expression:
Bent bonds (Section 2.11): The bonds in small rings such as cyclopropane that bend away from the internuclear line and overlap at a slight angle, rather than head-on. Bent bonds are highly strained and highly reactive.
Benzoyl (Section 10.1): The C₆H₅CO⁻ group.
Benzyl (Section 8.2): The C₆H₅CH₂⁻ group.
Benzylic (Section7.5): The position next to an aromatic ring.
β Lactam (Chapter 11 Chemistry Matters): A four-membered lactam, or cyclic amide. Penicillin and cephalosporin antibiotics contain β-lactam rings.
Bimolecular reaction (Section 7.2): A reaction whose rate-limiting step occurs between two reactants.
Boat cyclohexane (Section 2.12): A conformation of cyclohexane that bears a slight resemblance to a boat. Boat cyclohexane has no angle strain but has a large number of eclipsing interactions that make it less stable than chair cyclohexane.
Bond angle (Section 1.6): The angle formed between two adjacent bonds.
Bond dissociation energy, D (Section 4.8): The amount of energy needed to break a bond and produce two radical fragments.
Bond length (Section 1.5): The equilibrium distance between the nuclei of two atoms that are bonded to each other.
Bond strength (Section 1.5): An alternative name for bond dissociation energy.
Bonding MO (Section 1.11): A molecular orbital that is lower in energy than the atomic orbitals from which it is formed.
Branched-chain alkanes (Section 2.2): Alkanes that contain a branching connection of carbons as opposed to straight-chain alkanes.
Bromonium ion (Section 5.4): A species with a divalent, positively charged bromine, R₂Br⁺.
Brønsted–Lowry acid (Section 1.17): A substance that donates a hydrogen ion (proton; H⁺) to a base.
Brønsted–Lowry base (Section 1.17): A substance that accepts H⁺ from an acid.

Cahn–Ingold–Prelog sequence rules (Section 3.5, Section 4.4): A series of rules for assigning relative rankings to substituent groups on a chirality center or a double- bond carbon atom.
Cannizzaro reaction (Section 10.10): The disproportionation reaction of an aldehyde on treatment with base to yield an alcohol and a carboxylic acid.
Carbanion (Section 6.4, Section 10.7): A carbon anion, or substance that contains a trivalent, negatively charged carbon atom (R₃C:⁻). Alkyl carbanions are sp³– hybridized and have eight electrons in the outer shell of the negatively charged carbon.
Carbinolamine (Section 10.8): A molecule that contains the R₂C(OH)NH₂ functional group. Carbinolamines are produced as intermediates during the nucleophilic addition of amines to carbonyl compounds.
Carbocation (Section 4.7, Section 5.4): A carbon cation, or substance that contains a trivalent, positively charged carbon atom having six electrons in its outer shell (R₃C⁺).
Carbonyl group (Section 2.1, Preview of Carbonyl Chemistry): The C═O functional group.
Carboxyl group (Section 11.1): The −CO₂H functional group.
Carboxylation (Section 11.4): The addition of CO₂ to a molecule.
Carboxylic acids, RCO2H (Section 2.1, Chapter 11 Introduction): Compounds containing the −CO₂H functional group.
Carboxylic acid derivative (Chapter 11 Introduction): A compound in which an acyl group is bonded to an electronegative atom or substituent that can act as a leaving group in a substitution reaction. Esters, amides, and acid halides are examples.
Catalyst (Section 4.9): A substance that increases the rate of a chemical transformation by providing an alternative mechanism but is not itself changed in the reaction.
Chain-growth polymers (Section 5.7, Section 11.13): Polymers whose bonds are produced by chain reaction mechanisms. Polyethylene and other alkene polymers are examples.
Chair conformation (Section 2.12): A three-dimensional conformation of cyclohexane that resembles the rough shape of a chair. The chair form of cyclohexane is the lowest-energy conformation of the molecule.
Chiral (Section 3.2): Having handedness. Chiral molecules are those that do not have a plane of symmetry and are therefore not superimposable on their mirror image. A chiral molecule thus exists in two forms, one right-handed and one left- handed. The most common cause of chirality in a molecule is the presence of a carbon atom that is bonded to four different substituents.
Chiral environment (Section 3.10): The chiral surroundings or conditions in which a molecule resides.
Chirality center (Section 7.9): An atom (usually carbon) that is bonded to four different groups.
Cis–trans isomers (Section 2.9, Section 4.2 and 4.3): Stereoisomers that differ in their stereochemistry about a ring or double bond.
Combinatorial chemistry (Chapter 8 Chemistry Matters): A procedure in which anywhere from a few dozen to several hundred thousand substances are prepared simultaneously.
Condensed structures (Section 1.12): A shorthand way of writing structures in which carbon–hydrogen and carbon–carbon bonds are understood rather than shown explicitly. Propane, for example, has the condensed structure CH₃CH₂CH₃.
Configuration (Section 3.5): The three-dimensional arrangement of atoms bonded to a chirality center.
Conformations (Section 2.7): The three-dimensional shape of a molecule at any given instant, assuming that rotation around single bonds is frozen.
Conformational analysis (Section 2.15): A means of assessing the energy of a substituted cycloalkane by totaling the steric interactions present in the molecule.
Conformers (Section 2.7): Conformational isomers.
Conjugate acid (Section 1.17): The product that results from protonation of a Brønsted–Lowry base.
Conjugate base (Section 1.17): The product that results from deprotonation of a Brønsted–Lowry acid.
Conjugation (Chapter 5 Introduction): A series of overlapping p orbitals, usually in alternating single and multiple bonds. For example, 1,3-butadiene is a conjugated diene, 3-buten-2-one is a conjugated enone, and benzene is a cyclic conjugated triene.
Constitutional isomers (Section 2.2, Section 2.7, Section 3.9): Isomers that have their atoms connected in a different order. For example, butane and 2- methylpropane are constitutional isomers.
Covalent bond (Section 1.4, Section 1.5): A bond formed by sharing electrons between atoms.
Cracking (Chapter 2 Chemistry Matters): A process used in petroleum refining in which large alkanes are thermally cracked into smaller fragments.
Curtius rearrangement (Section 12.4): The conversion of an acid chloride into an amine by reaction with azide ion, followed by heating with water.
Cyanohydrins (Section 10.6): A class of compounds with an −OH group and a −CN group bonded to the same carbon atom; formed by addition of HCN to an aldehyde or ketone.
Cycloalkane (Section 2.5): An alkane that contains a ring of carbons.

d,l form (Section 3.8): The racemic mixture of a chiral compound.
Deactivating groups (Section 8.6): Electron-withdrawing substituents that decrease the reactivity of an aromatic ring toward electrophilic aromatic substitution.
Debyes (D) (Section 1.13): Units for measuring dipole moments; 1 D = 3.336 × 10⁻³⁰ coulomb meter (C ∙ m).
Degenerate orbitals (Section 8.1): Two or more orbitals that have the same energy level.
Dehydration (Section 5.7, Section 9.7): The loss of water from an alcohol to yield an alkene.
Dehydrohalogenation (Section 5.7, Section 4.1): The loss of HX from an alkyl halide. Alkyl halides undergo dehydrohalogenation to yield alkenes on treatment with strong base.
Delocalization (Section 8.1): A spreading out of electron density over a conjugated π electron system. For example, allylic cations and allylic anions are delocalized because their charges are spread out over the entire π electron system. Aromatic compounds have 4n + 2 π electrons delocalized over their ring.
Dess–Martin periodinane (Section 9.8): An iodine-based reagent commonly used for the laboratory oxidation of a primary alcohol to an aldehyde or a secondary alcohol to a ketone.
Deuterium isotope effect (Section 7.8): A tool used in mechanistic investigations to establish whether a C−H bond is broken in the rate-limiting step of a reaction.
Dextrorotatory (Section 3.3): A word used to describe an optically active substance that rotates the plane of polarization of plane-polarized light in a right-handed (clockwise) direction.
Diastereomers (Section 3.6): Non–mirror-image stereoisomers; diastereomers have the same configuration at one or more chirality centers but differ at other chirality centers.
1,3-Diaxial interaction (Section 2.14): The strain energy caused by a steric interaction between axial groups three carbon atoms apart in chair cyclohexane.
Dihedral angle (Section 2.7): The angle between two bonds on adjacent carbons as viewed along the C−C bond.
Dipole moment, µ (Section 1.13): A measure of the net polarity of a molecule. A dipole moment arises when the centers of mass of positive and negative charges within a molecule do not coincide.
Dipole–dipole forces (Section 1.22): Noncovalent electrostatic interactions between dipolar molecules.
Dispersion forces (Section 1.22): Noncovalent interactions between molecules that arise because of constantly changing electron distributions within the molecules.
Disulfides (RSSR′) (Section 9.15): A class of compounds of the general structure RSSR′.
Double bond (Section 1.8): A covalent bond formed by sharing two electron pairs between atoms.

E geometry (Section 4.4): A term used to describe the stereochemistry of a carbon– carbon double bond. The two groups on each carbon are ranked according to the Cahn–Ingold–Prelog sequence rules, and the two carbons are compared. If the higher-ranked groups on each carbon are on opposite sides of the double bond, the bond has E geometry.
E1 reaction (Section 7.10): A unimolecular elimination reaction in which the substrate spontaneously dissociates to give a carbocation intermediate, which loses a proton in a separate step.
E1cB reaction (Section 7.10): A unimolecular elimination reaction in which a proton is first removed to give a carbanion intermediate, which then expels the leaving group in a separate step.
E2 reaction (Section 7.8): A bimolecular elimination reaction in which C−H and C−X bond cleavages are simultaneous.
Eclipsed conformation (Section 2.7): The geometric arrangement around a carbon–carbon single bond in which the bonds to substituents on one carbon are parallel to the bonds to substituents on the neighboring carbon as viewed in a Newman projection.
Eclipsing strain (Section 2.7): The strain energy in a molecule caused by electron repulsions between eclipsed bonds. Eclipsing strain is also called torsional strain.
Electron configuration (Section 1.3): A list of the orbitals occupied by electrons in an atom.
Electron-dot structure (Section 1.4): A representation of a molecule showing valence electrons as dots.
Electron shells (Section 1.2): A group of an atom’s electrons with the same principal quantum number.
Electronegativity (EN) (Section 1.12): The ability of an atom to attract electrons in a covalent bond. Electronegativity increases across the periodic table from left to right and from bottom to top.
Electrophile (Section 4.6, Section 4.7): An “electron-lover,” or substance that accepts an electron pair from a nucleophile in a polar bond-forming reaction.
Electrophilic addition reactions (Section 5.1): Addition of an electrophile to a carbon–carbon double bond to yield a saturated product.
Electrophilic aromatic substitution reaction (Chapter 8 Introduction): A reaction in which an electrophile (E⁺) reacts with an aromatic ring and substitutes for one of the ring hydrogens.
Electrostatic potential maps (Section 1.12): Molecular representations that use color to indicate the charge distribution in molecules as derived from quantum- mechanical calculations.
Elimination reactions (Section 4.5): What occurs when a single reactant splits into two products.
Enamines (Section 10.8): Compounds with the R₂N–CR═CR₂ functional group.
Enantiomers (Section 3.1): Stereoisomers of a chiral substance that have a mirror- image relationship. Enantiomers have opposite configurations at all chirality centers.
Enantioselective synthesis (Chapter 10 Chemistry Matters): A reaction method that yields only a single enantiomer of a chiral product starting from an achiral reactant.
Endergonic (Section 4.8): A reaction that has a positive free-energy change and is therefore nonspontaneous. In an energy diagram, the product of an endergonic reaction has a higher energy level than the reactants.
Endothermic (Section 4.8): A reaction that absorbs heat and therefore has a positive enthalpy change.
Energy diagram (Section 6.8): A representation of the course of a reaction, in which free energy is plotted as a function of reaction progress. Reactants, transition states, intermediates, and products are represented, and their appropriate energy levels are indicated.
Enol (Section 5.10): A vinylic alcohol that is in equilibrium with a carbonyl compound, C═C–OH.
Enthalpy change (ΔH) (Section 4.9): The heat of reaction. The enthalpy change that occurs during a reaction is a measure of the difference in total bond energy between reactants and products.
Entropy change (ΔS) (Section 4.9): The change in amount of molecular randomness. The entropy change that occurs during a reaction is a measure of the difference in randomness between reactants and products.
Epimers (Section 3.6): Diastereomers that differ in configuration at only one chirality center but are the same at all others.
Epoxide (Section 5.6): A three-membered-ring ether functional group.
Equatorial bonds (Section 2.13): Bonds or positions in chair cyclohexane that lie along the rough equator of the ring.
Essential oil (Chapter 5 Chemistry Matters): The volatile oil obtained by steam distillation of a plant extract.
Esters (Section 2.1, Chapter 11 Introduction): A class of compounds containing the −CO₂R functional group.
Ethers (Section 2.1): A class of compounds that has two organic substituents bonded to the same oxygen atom, ROR′.

First-order reaction (Section 7.4): Designates a reaction whose rate-limiting step is unimolecular and whose kinetics therefore depend on the concentration of only one reactant.
Fischer esterification reaction (Section 11.6): The acid-catalyzed nucleophilic acyl substitution reaction of a carboxylic acid with an alcohol to yield an ester.
Formal charges (Section 1.14): The difference in the number of electrons owned by an atom in a molecule and by the same atom in its elemental state.
Formyl (Section 10.1): A −CHO group.
Friedel–Crafts reaction (Section 8.5): An electrophilic aromatic substitution reaction to alkylate or acylate an aromatic ring.
Functional (Section 2.1): An atom or group of atoms that is part of a larger molecule and has a characteristic chemical reactivity.

Gabriel amine synthesis (Section 12.4): A method for preparing an amine by S_N2 reaction of an alkyl halide with potassium phthalimide, followed by hydrolysis.
Gauche conformation (Section 2.8): The conformation of butane in which the two methyl groups lie 60° apart as viewed in a Newman projection. This conformation has 3.8 kJ/mol steric strain.
Geminal (Section 10.5): Referring to two groups attached to the same carbon atom. For example, the hydrate formed by nucleophilic addition of water to an aldehyde or ketone is a geminal diol.
Glycol (Section 5.6): A diol, such as ethylene glycol, HOCH₂CH₂OH.
Green chemistry (Chapter 7 Chemistry Matters): The design and implementation of chemical products and processes that reduce waste and minimize or eliminate the generation of hazardous substances.
Grignard reagent (RMgX) (Section 6.4): An organomagnesium halide.
Ground-state electron configuration (Section 1.3): The most stable, lowest- energy electron configuration of a molecule or atom.

Halogenation (Section 5.4, Section 8.3): The reaction of halogen with an alkene to yield a 1,2-dihalide addition product or with an aromatic compound to yield a substitution product.
Halonium ion (Section 5.4): A species containing a positively charged, divalent halogen. Three-membered-ring bromonium ions are intermediates in the electrophilic addition of Br₂ to alkenes.
Heat of combustion (Section 2.10): The amount of heat released when a compound burns completely in oxygen.
Heat of hydrogenation (Section 4.3): The amount of heat released when a carbon– carbon double bond is hydrogenated.
Hemiacetal (Section 10.6): A functional group having one −OR and one −OH group bonded to the same carbon.
Heterocycle (Section 8.9, Section 12.6): A cyclic molecule whose ring contains more than one kind of atom. For example, pyridine is a heterocycle that contains five carbon atoms and one nitrogen atom in its ring.
Heterolytic bond breakage (Section 4.6): The kind of bond-breaking that occurs in polar reactions when one fragment leaves with both of the bonding electrons: A : B → A⁺ + B:⁻.
Hofmann elimination reaction (Section 12.5): The elimination reaction of an amine to yield an alkene by reaction with iodomethane followed by heating with Ag₂O.
Hofmann rearrangement (Section 12.4): The conversion of an amide into an amine by reaction with Br₂ and base.
Homolytic bond breakage (Section 4.6): The kind of bond-breaking that occurs in radical reactions when each fragment leaves with one bonding electron: A : B → A· + B·.
Hund’s rule (Section 1.3): If two or more empty orbitals of equal energy are available, one electron occupies each, with their spins parallel, until all are half-full.
Hybrid orbital (Section 1.6): An orbital derived from a combination of atomic orbitals. Hybrid orbitals, such as the sp³, sp², and sp hybrids of carbon, are strongly directed and form stronger bonds than atomic orbitals do.
Hydration (Section 5.3): Addition of water to a molecule, such as occurs when alkenes are treated with aqueous sulfuric acid to give alcohols.
Hydride shift (Section 4.6): The shift of a hydrogen atom and its electron pair to a nearby cationic center.
Hydroboration (Section 5.5): Addition of borane (BH₃) or an alkylborane to an alkene. The resultant trialkylborane products can be oxidized to yield alcohols.
Hydrocarbons (Section 2.2): A class of compounds that contain only carbon and hydrogen.
Hydrogen bond (Section 1.22): A weak attraction between a hydrogen atom bonded to an electronegative atom and an electron lone pair on another electronegative atom.
Hydrogenated (Section 4.6): Addition of hydrogen to a double or triple bond to yield a saturated product.
Hydrophilic (Section 1.22): Water-loving; attracted to water.
Hydrophobic (Section 1.22): Water-fearing; repelled by water.
Hydroquinones (Section 9.10): 1,4-dihydroxybenzene.
Hydroxylation (Section 5.6): Addition of two −OH groups to a double bond.
Hyperconjugation (Section 4.3, Section 5.2): An electronic interaction that results from overlap of a vacant p orbital on one atom with a neighboring C−H σ bond. Hyperconjugation is important in stabilizing carbocations and substituted alkenes.

Imide (Section 12.4): A compound with the −CONHCO− functional group.
Imines (Section 10.8): A class of compounds with the R₂C═NR functional group.
Inductive effect (Section 1.12, Section 5.2, Section 8.6): The electron-attracting or electron-withdrawing effect transmitted through σ bonds. Electronegative elements have an electron-withdrawing inductive effect.
Initiator (Section 5.7): A substance that is used to initiate a radical chain reaction or polymerization. For example, radical chlorination of alkanes is initiated when light energy breaks the weak Cl−Cl bond to form Cl· radicals.
Intermediate (Section 4.9): A species that is formed during the course of a multistep reaction but is not the final product. Intermediates are more stable than transition states but may or may not be stable enough to isolate.
Ion pairs (Section 7.4): A loose association between two ions in solution. Ion pairs are implicated as intermediates in S_N1 reactions to account for the partial retention of stereochemistry that is often observed.
Ionic bond (Section 1.4): The electrostatic attraction between ions of unlike charge.
Isomers (Section 2.2, Section 3.9): Compounds that have the same molecular formula but different structures.
Isoprene rule (Chapter 5 Chemistry Matters): An observation to the effect that terpenoids appear to be made up of isoprene (2-methyl-1,3-butadiene) units connected head-to-tail.
Isotopes (Section 1.1): Atoms of the same element that have different mass numbers.
IUPAC system of nomenclature (Section 2.4): Rules for naming compounds, devised by the International Union of Pure and Applied Chemistry.

Kekulé structure (Section 1.4): An alternative name for a line-bond structure, which represents a molecule by showing covalent bonds as lines between atoms.
Ketals (Section 10.9): An alternative name for acetals derived from a ketone rather than an aldehyde and consisting of two −OR groups bonded to the same carbon, R₂C(OR′)₂. Ketals are often used as protecting groups for ketones.
Ketones (R₂CO) (Section 2.1, Chapter 10 Introduction): A class of compounds with two organic substituents bonded to a carbonyl group, R₂C═O.
Kinetics (Section 7.2): Referring to reaction rates. Kinetic measurements are useful for helping to determine reaction mechanisms.

Lactams (Section 11.10): Cyclic amides.
Lactones (Section 11.9): Cyclic esters.
LD50 (Chapter 1 Chemistry Matters): The amount of a substance per kilogram body weight that is lethal to 50% of test animals.
Leaving group (Section 7.3): The group that is replaced in a substitution reaction.
Levorotatory (Section 3.3): An optically active substance that rotates the plane of polarization of plane-polarized light in a left-handed (counterclockwise) direction.
Lewis acid (Section 1.21): A substance with a vacant low-energy orbital that can accept an electron pair from a base. All electrophiles are Lewis acids.
Lewis base (Section 1.21): A substance that donates an electron lone pair to an acid. All nucleophiles are Lewis bases.
Lewis structures (Section 1.4): Representations of molecules showing valence electrons as dots.
Lindlar catalyst (Section 5.12): A hydrogenation catalyst used to convert alkynes to cis alkenes.
Line-bond structure (Section 1.4): An alternative name for a Kekulé structure, which represents a molecule by showing covalent bonds as lines between atoms.
Locant (Section 2.4): A number in a chemical name that locates the positions of the functional groups and substituents in the molecule.
Lone-pair electrons (Section 1.4): Nonbonding valence-shell electron pairs. Lone- pair electrons are used by nucleophiles in their reactions with electrophiles.

Markovnikov’s rule (Section 5.1): A guide for determining the regiochemistry (orientation) of electrophilic addition reactions. In the addition of HX to an alkene, the hydrogen atom bonds to the alkene carbon that has fewer alkyl substituents.
Mass number (A) (Section 1.1): The total of protons plus neutrons in an atom.
McLafferty rearrangement (Section 10.4): A mass-spectral fragmentation pathway for carbonyl compounds.
Mechanism (Section 4.6): A complete description of how a reaction occurs. A mechanism accounts for all starting materials and all products and describes the details of each individual step in the overall reaction process.
Mercapto group (Section 9.15): An alternative name for the thiol group, −SH.
Meso compounds (Section 3.7): Compounds that contain chirality centers but are nevertheless achiral because they contain a symmetry plane.
Meta (m) (Section 8.2): A naming prefix used for 1,3-disubstituted benzenes.
Methylene group (Section 4.1): A −CH₂− or ═CH₂ group.
Molecular mechanics (Chapter 2 Chemistry Matters): A computer-based method for calculating the minimum-energy conformation of a molecule.
Molecular orbital (MO) theory (Section 5.8): A description of covalent bond formation as resulting from a mathematical combination of atomic orbitals (wave functions) to form molecular orbitals.
Molecule (Section 1.4): A neutral collection of atoms held together by covalent bonds.
Monomers (Section 5.7, Section 11.13): The simple starting units from which polymers are made.
Monoterpenoids (Chapter 5 Chemistry Matters): Ten-carbon lipids

Natural gas (Chapter 2 Chemistry Matters): A naturally occurring hydrocarbon mixture consisting chiefly of methane, along with smaller amounts of ethane, propane, and butane.
Natural product (Chapter 5 Chemistry Matters): A catchall term generally taken to mean a secondary metabolite found in bacteria, plants, and other living organisms.
New molecular entity, NME (Chapter 4 Chemistry Matters): A new biologically active chemical substance approved for sale as a drug by the U.S. Food and Drug Administration.
Newman projection (Section 2.7): A means of indicating stereochemical relationships between substituent groups on neighboring carbons. The carbon– carbon bond is viewed end-on, and the carbons are indicated by a circle. Bonds radiating from the center of the circle are attached to the front carbon, and bonds radiating from the edge of the circle are attached to the rear carbon.
Nitration (Section 8.4): The substitution of a nitro group onto an aromatic ring.
Nitriles (Section 2.1, Section 11.1): A class of compounds containing the C≡N functional group.
Node (Section 1.2): A surface of zero electron density within an orbital. For example, a p orbital has a nodal plane passing through the center of the nucleus, perpendicular to the axis of the orbital.
Nonbonding electrons (Section 1.4): Valence electrons that are not used in forming covalent bonds.
Noncovalent interactions (Section 1.22): One of a variety of nonbonding interactions between molecules, such as dipole–dipole forces, dispersion forces, and hydrogen bonds.
Normal alkanes (Section 2.2): Straight-chain alkanes, as opposed to branched alkanes. Normal alkanes are denoted by the suffix n, as in n-C₄H₁₀ (n-butane).
NSAID (Chapter 8 Chemistry Matters): A nonsteroidal anti-inflammatory drug, such as aspirin or ibuprofen.
Nucleophile (Section 4.6, Section 4.7): An electron-rich species that donates an electron pair to an electrophile in a polar bond-forming reaction. Nucleophiles are also Lewis bases.
Nucleophilic acyl substitution reaction (Section 11.5): A reaction in which a nucleophile attacks a carbonyl compound and substitutes for a leaving group bonded to the carbonyl carbon.
Nucleophilic addition reaction (Section 10.4): A reaction in which a nucleophile adds to the electrophilic carbonyl group of a ketone or aldehyde to give an alcohol.
Nucleophilic substitution reactions (Section 7.1): Reactions in which one nucleophile replaces another attached to a saturated carbon atom.
Nucleophilicity (Section 7.3): The ability of a substance to act as a nucleophile in an S_N2 reaction.
Nylons (Section 11.13): Synthetic polyamide step-growth polymers.

Olefin (Chapter 5 Introduction): An alternative name for an alkene.
Optical isomers (Section 3.4): An alternative name for enantiomers. Optical isomers are isomers that have a mirror-image relationship.
Optically active (Section 3.3): A property of some organic molecules wherein the plane of polarization is rotated through an angle when a beam of plane-polarized light is passed through a solution of the molecules.
Orbital (Section 1.2): A wave function, which describes the volume of space around a nucleus in which an electron is most likely to be found.
Organic chemistry (Chapter 1 Introduction): The study of carbon compounds.
Organohalides (Chapter 6 Introduction): Compounds that contain one or more halogen atoms bonded to carbon.
Organometallic compound (Section 6.4): A compound that contains a carbon– metal bond. Grignard reagents, RMgX, are examples.
Organophosphate (Section 1.10): A compound that contains a phosphorus atom bonded to four oxygens, with one of the oxygens also bonded to carbon.
Ortho (o) (Section 8.2): A naming prefix used for 1,2-disubstituted benzenes.
Oxidation (Section 5.6, Section 6.5): A reaction that causes a decrease in electron ownership by carbon, either by bond formation between carbon and a more electronegative atom (usually oxygen, nitrogen, or a halogen) or by bond-breaking between carbon and a less electronegative atom (usually hydrogen).
Oximes (Section 10.8): Compounds with the R₂C═NOH functional group.
Oxirane (Section 5.6): An alternative name for an epoxide.

Para (p) (Section 8.2): A naming prefix used for 1,4-disubstituted benzenes.
Paraffins (Section 2.6): A common name for alkanes.
Pauli exclusion principle (Section 1.3): No more than two electrons can occupy the same orbital, and those two must have spins of opposite sign.
Periplanar (Section 7.8): A conformation in which bonds to neighboring atoms have a parallel arrangement. In an eclipsed conformation, the neighboring bonds are syn periplanar; in a staggered conformation, the bonds are anti periplanar.
Peroxides (Section 9.3): Molecules containing an oxygen–oxygen bond functional group, ROOR′ or ROOH.
Peroxyacid (Section 5.6): A compound with the −CO₃H functional group. Peroxyacids react with alkenes to give epoxides.
Phenols (Chapter 9 Introduction): A class of compounds with an −OH group directly bonded to an aromatic ring, ArOH.
Phenoxide ion, ArO− (Section 9.2): The anion of a phenol.
Phenyl (Section 8.2): The name for the −C₆H₅ unit when the benzene ring is considered as a substituent. A phenyl group is abbreviated as −Ph.
Pi (π) bond (Section 1.8): The covalent bond formed by sideways overlap of atomic orbitals. For example, carbon–carbon double bonds contain a π bond formed by sideways overlap of two p orbitals.
pK_a (Section 1.18): The negative common logarithm of the K_a; used to express acid strength.
Plane of symmetry (Section 3.2): A plane that bisects a molecule such that one half of the molecule is the mirror image of the other half. Molecules containing a plane of symmetry are achiral.
Plane-polarized light (Section 3.3): Light that has its electromagnetic waves oscillating in a single plane rather than in random planes. The plane of polarization is rotated when the light is passed through a solution of a chiral substance.
Polar aprotic solvents (Section 7.3): Polar solvents that can’t function as hydrogen ion donors. Polar aprotic solvents such as dimethyl sulfoxide (DMSO) and dimethylformamide (DMF) are particularly useful in S_N2 reactions because of their ability to solvate cations.
Polar covalent bond (Section 1.12): A covalent bond in which the electron distribution between atoms is unsymmetrical.
Polar reactions (Section 4.6): Reactions in which bonds are made when a nucleophile donates two electrons to an electrophile and in which bonds are broken when one fragment leaves with both electrons from the bond.
Polarity (Section 1.12): The unsymmetrical distribution of electrons in a molecule that results when one atom attracts electrons more strongly than another.
Polarizability (Section 4.6): The measure of the change in a molecule’s electron distribution in response to changing electrostatic interactions with solvents or ionic reagents.
Polycyclic aromatic compound (Section 8.9): A compound with two or more benzene-like aromatic rings fused together.
Polymer (Section 5.7, Section 11.13): A large molecule made up of repeating smaller units. For example, polyethylene is a synthetic polymer made from repeating ethylene units, and DNA is a biopolymer made of repeating deoxyribonucleotide units.
Primary, secondary, tertiary, and quaternary (Section 2.3): Terms used to describe the substitution pattern at a specific site. A primary site has one organic substituent attached to it, a secondary site has two organic substituents, a tertiary site has three, and a quaternary site has four.
Propagation step (Section 5.7): A step in a radical chain reaction that carries on the chain. The propagation steps must yield both product and a reactive intermediate.
Protecting group (Section 10.9): A group that is introduced to protect a sensitive functional group toward reaction elsewhere in the molecule. After serving its protective function, the group is removed.
Protic solvents (Section 7.3): Solvents such as water or alcohol that can act as a proton donor.
Pyramidal inversion (Section 12.2): The rapid stereochemical inversion of a trivalent nitrogen compound.

Quaternary ammonium salt (Section 12.1): An ionic compound containing a positively charged nitrogen atom with four attached groups, R⁴N⁺ X⁻.
Quinone (Section 9.10): A 2,5-cyclohexadiene-1,4-dione.

R configuration (Section 3.5): The configuration at a chirality center as specified using the Cahn–Ingold–Prelog sequence rules.
R (Section 2.3): A generalized abbreviation for an organic partial structure.
Racemate (Section 3.8): A mixture consisting of equal parts (+) and (−) enantiomers of a chiral substance; also called a racemic mixture.
Radical (Section 2.6, Section 4.6): A species that has an odd number of electrons, such as the chlorine radical, Cl·.
Radical reactions (Section 4.6): Reactions in which bonds are made by donation of one electron from each of two reactants and in which bonds are broken when each fragment leaves with one electron.
Rate constant (Section 7.2): The constant k in a rate equation.
Rate equation (Section 7.2): An equation that expresses the dependence of a reaction’s rate on the concentration of reactants.
Rate-limiting step (Section 7.4): The slowest step in a multistep reaction sequence; also called the rate-determining step. The rate-limiting step acts as a kind of bottleneck in multistep reactions.
Rearrangement reactions (Section 4.5): What occurs when a single reactant undergoes a reorganization of bonds and atoms to yield an isomeric product.
Reduction (Section 5.5, Section 6.5): A reaction that causes an increase of electron ownership by carbon, either by bond-breaking between carbon and a more electronegative atom or by bond formation between carbon and a less electronegative atom.
Reductive amination (Section 12.4): A method for preparing an amine by reaction of an aldehyde or ketone with ammonia and a reducing agent.
Refining (Chapter 2 Chemistry Matters): The process by which petroleum is converted into gasoline and other useful products.
Regiochemistry (Section 5.1): A term describing the orientation of a reaction that occurs on an unsymmetrical substrate.
Regiospecific (Section 5.1): A term describing a reaction that occurs with a specific regiochemistry to give a single product rather than a mixture of products.
Resolution (Section 3.8): The process by which a racemate is separated into its two pure enantiomers.
Resonance effect (Section 8.6): The donation or withdrawal of electrons through orbital overlap with neighboring π bonds. For example, an oxygen or nitrogen substituent donates electrons to an aromatic ring by overlap of the O or N orbital with the aromatic ring p orbitals.
Resonance forms (Section 1.15): Individual structural forms of a resonance hybrid.
Resonance hybrid (Section 1.15): A molecule, such as benzene, that can’t be represented adequately by a single Kekulé structure but must instead be considered as an average of two or more resonance forms. The resonance forms themselves differ only in the positions of their electrons, not their nuclei.
Ring-flip (Section 2.13): A molecular motion that interconverts two chair conformations of cyclohexane. The effect of a ring-flip is to convert an axial substituent into an equatorial substituent.

S configuration (Section 3.5): The configuration at a chirality center as specified using the Cahn–Ingold–Prelog sequence rules.
Saponification (Section 11.9): An old term for the base-induced hydrolysis of an ester to yield a carboxylic acid salt.
Saturated (Section 2.2): A molecule that has only single bonds and thus can’t undergo addition reactions. Alkanes are saturated, but alkenes are unsaturated.
Sawhorse representations (Section 2.7): A manner of representing stereochemistry that uses a stick drawing and gives a perspective view of the conformation around a single bond.
Schiff bases (Section 10.8): An alternative name for an imine, R₂C═NR′, used primarily in biochemistry.
Second-order reaction (Section 7.2): A reaction whose rate-limiting step is bimolecular and whose kinetics are therefore dependent on the concentration of two reactants.
Secondary metabolite (Chapter 5 Chemistry Matters): A small naturally occurring molecule that is not essential to the growth and development of the producing organism and is not classified by structure.
Sequence rules (Section 3.5, Section 4.4): A series of rules for assigning relative rankings to substituent groups on a double-bond carbon atom or on a chirality center.
Sharpless epoxidation (Chapter 10 Chemistry Matters): A method for enantioselective synthesis of a chiral epoxide by treatment of an allylic alcohol with tert-butyl hydroperoxide, (CH₃)₃C–OOH, in the presence of titanium tetraisopropoxide and diethyl tartrate.
Sigma (σ) bond (Section 1.5): A covalent bond formed by head-on overlap of atomic orbitals.
Single bond (Section 1.8): A covalent bond formed by sharing one electron pair between atoms.
Skeletal structures (Section 1.12): A shorthand way of writing structures in which carbon atoms are assumed to be at each intersection of two lines (bonds) and at the end of each line.
S_N1 reaction (Section 7.4): A unimolecular nucleophilic substitution reaction.
S_N2 reaction (Section 7.2): A bimolecular nucleophilic substitution reaction.
Solvation (Section 7.3): The clustering of solvent molecules around a solute particle to stabilize it.
sp hybrid orbitals (Section 1.9): Hybrid orbitals derived from the combination of an s and a p atomic orbital. The two sp orbitals that result from hybridization are oriented at an angle of 180° to each other.
sp²hybrid orbitals (Section 1.8): Hybrid orbitals derived by combination of an s atomic orbital with two p atomic orbitals. The three sp² hybrid orbitals that result lie in a plane at angles of 120° to each other.
sp³hybrid orbitals (Section 1.6): Hybrid orbitals derived by combination of an s atomic orbital with three p atomic orbitals. The four sp³ hybrid orbitals that result are directed toward the corners of a regular tetrahedron at angles of 109° to each other.
Specific rotation, [α]_D (Section 3.3): The optical rotation of a chiral compound under standard conditions.
Staggered conformation (Section 2.7): The three-dimensional arrangement of atoms around a carbon–carbon single bond in which the bonds on one carbon bisect the bond angles on the second carbon as viewed end-on.
Step-growth polymers (Section 11.13): Polymers in which each bond is formed independently of the others. Polyesters and polyamides (nylons) are examples.
Stereocenter (Section 3.2): An alternative name for a chirality center.
Stereochemistry (Section 2.6; Chapters 2): The branch of chemistry concerned with the three-dimensional arrangement of atoms in molecules.
Stereogenic center (Section 3.2): An alternative name for a chirality center.
Stereoisomers (Section 2.9): Isomers that have their atoms connected in the same order but have different three-dimensional arrangements. The term stereoisomer includes both enantiomers and diastereomers.
Steric strain (Section 2.8, Section 2.10, Section 2.14): The strain imposed on a molecule when two groups are too close together and try to occupy the same space. Steric strain is responsible both for the greater stability of trans versus cis alkenes and for the greater stability of equatorially substituted versus axially substituted cyclohexanes.
Straight-chain alkanes (Section 2.2): Alkanes whose carbon atoms are connected without branching.
Substitution reactions (Section 4.5): What occurs when two reactants exchange parts to give two new products. S_N1 and S_N2 reactions are examples.
Sulfides (Section 2.1, Section 9.15): A class of compounds that has two organic substituents bonded to the same sulfur atom, RSR′.
Sulfonation (Section 8.4): The substitution of a sulfonic acid group (−SO₃H) onto an aromatic ring.
Sulfone (Section 9.15): A compound of the general structure RSO₂R′.
Sulfonium ions (Section 9.15): A species containing a positively charged, trivalent sulfur atom, R₃S⁺.
Sulfoxide (Section 9.15): A compound of the general structure RSOR′.
Symmetry plane (Section 3.2): A plane that bisects a molecule such that one half of the molecule is the mirror image of the other half. Molecules containing a plane of symmetry are achiral.
Syn periplanar (Section 7.8): Describing a stereochemical relationship in which two bonds on adjacent carbons lie in the same plane and are eclipsed.
Syn stereochemistry (Section 5.3): The opposite of anti. A syn addition reaction is one in which the two ends of the double bond react from the same side. A syn elimination is one in which the two groups leave from the same side of the molecule

Terpenoids (Chapter 5 Chemistry Matters): Lipids that are formally derived by head-to-tail polymerization of isoprene units.
Thioesters (Chapter 11 Introduction): A class of compounds with the RCOSR′ functional group.
Thiols (Section 2.1, Chapter 9 Introduction): A class of compounds containing the −SH functional group.
Thiolate ion (Section 9.15): The anion of a thiol, RS⁻.
Torsional strain (Section 2.7, Section 2.10): The strain in a molecule caused by electron repulsion between eclipsed bonds. Torsional strain is also called eclipsing strain.
Tosylate (Section 7.1): A p-toluenesulfonate ester; useful as a leaving group in nucleophilic substitution reactions.
Transition state (Section 4.8): An activated complex between reactants, representing the highest energy point on a reaction curve. Transition states are unstable complexes that can’t be isolated.
Triple bonds (Section 1.8): A type of covalent bond formed by sharing three electron pairs between atoms.
Twist-boat conformation (Section 2.12): A conformation of cyclohexane that is somewhat more stable than a pure boat conformation.

Unimolecular reaction (Section 7.4): A reaction that occurs by spontaneous transformation of the starting material without the intervention of other reactants. For example, the dissociation of a tertiary alkyl halide in the S_N1 reaction is a unimolecular process.
Unsaturated (Section 4.1): A molecule that has one or more multiple bonds.

Valence bond theory (Section 1.5): A bonding theory that describes a covalent bond as resulting from the overlap of two atomic orbitals.
Valence shell (Section 1.4): The outermost electron shell of an atom.
van der Waals forces (Section 1.22): Intermolecular forces that are responsible for holding molecules together in the liquid and solid states.
Vicinal (Section 4.1): A term used to refer to a 1,2-disubstitution pattern. For example, 1,2-dibromoethane is a vicinal dibromide.
Vinyl group (Section 4.1): A H₂C═CH– substituent.
Vinyl monomer (Section 5.7): A substituted alkene monomer used to make a chain-growth polymer.
Vinylic (Section 5.10): A term that refers to a substituent at a double-bond carbon atom. For example, chloroethylene is a vinylic chloride, and enols are vinylic alcohols.

Walden inversion (Section 7.1): The inversion of configuration at a chirality center that accompanies an S_N2 reaction.
Wave equation (Section 1.2): A mathematical expression that defines the behavior of an electron in an atom.
Wave function (Section 1.2): A solution to the wave equation for defining the behavior of an electron in an atom. The square of the wave function defines the shape of an orbital.
Williamson ether synthesis (Section 9.11): A method for synthesizing ethers by S_N2 reaction of an alkyl halide with an alkoxide ion.

Z geometry (Section 4.4): A term used to describe the stereochemistry of a carbon– carbon double bond. The two groups on each carbon are ranked according to the Cahn–Ingold–Prelog sequence rules, and the two carbons are compared. If the higher ranked groups on each carbon are on the same side of the double bond, the bond has Z geometry.
Zaitsev’s rule (Section 7.7): A rule stating that E2 elimination reactions normally yield the more highly substituted alkene as major product.

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Fundamentals of Organic Chemistry-OpenStax Adaptation Copyright © by Kirsten Kramer and Cassandra Lilly is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except where otherwise noted.

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