Jones M., Fleming S.A. Organic Chemistry

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NR NR

GLOSSARY G-9

is lower in energy than

Hückel’s rule (Section 13.6) All planar, cyclic, fully conjugated

molecules with 4n + 2 π electrons will be aromatic (especially

stable).The rule works because such molecules will have

molecular orbital systems in which all bonding molecular orbitals

are full and all antibonding molectular orbitals are empty. In such

molecules, the bonding degenerate molecular orbitals are filled.

Hund’s rule (Section 1.2) For a given electronic configuration, the

state with the greatest number of parallel spins is the lowest in

energy. That is,

Hunsdiecker reaction (Section 17.7) The conversion of silver

salts of carboxylic acids into alkyl halides, usually bromides.

Hybridization (Section 2.2) A mathematical model in which

atomic orbital wave functions are combined to produce new,

combination, or hybrid orbitals. The new orbitals are made up of

fractions of the pure atomic orbital wave functions.Thus, an sp

hybrid is made of three parts p wave function and one part s wave

function.

Hybrid orbitals (Section 2.2) Orbitals that result from

hybridization.

Hydrate (Section 16.6) The product of the reaction of a carbonyl

compound with water.

Hydration (Section 9.7) The addition of water to a molecule.

This reaction is generally acid catalyzed.

Hydride (Section 2.4) A negatively charged hydrogen ion (H

)

bearing a pair of electrons.

Hydride shift (Section 9.9) The migration of hydrogen with a

pair of electrons (H

Hydroboration (Section 9.10) The addition of BH

(in

equilibrium with the dimer B

) to π systems to form

alkylboranes. These alkylboranes can be further converted into

alcohols. Addition to an unsymmetrical alkene proceeds so as to

give the less substituted alcohol.

Hydrocarbon (Section 2.1) A molecule containing only carbon

and hydrogen.

Hydrocarbon cracking (Section 11.2) The thermal treatment of

high molecular weight hydrocarbons to give lower molecular

weight fragments. Bonds are broken to give radicals that abstract

hydrogen to give alkanes, undergo β-cleavage, and

disproportionate to give alkenes and alkanes.

Hydrogenation (Section 10.2) Addition of hydrogen (H

) to the

π bond of an alkene to give an alkane. A soluble or insoluble

metallic catalyst is necessary. Alkynes also undergo hydrogenation

to give alkanes, or under special conditions, alkenes.

Hydrogen bonding (Section 6.4) A low-energy bond between a

pair of electrons, usually on oxygen, and a hydrogen.

Hydrophilic (Section 17.8) “Water-loving,” hence a polar group

soluble in water.

Hydrophobic (Section 17.8) “Water-hating,”hence a nonpolar

group insoluble in water.

Hyperconjugation (Section 9.5) The stabilization of carbocations

through the overlap of a filled σ orbital with an empty 2p orbital

on carbon.

Imide (Section 18.2) A compound containing the structure

such asO

Imine (Section 16.11) The nitrogen analogue of a ketone or

aldehyde. See Schiff base.

Iminium ion (Section 16.11) A compound of the structure

Inductive effects (Section 9.6) Electronic effects transmitted

through σ bonds. All bonds between different atoms are polar,

and thus many molecules contain dipoles.These dipoles can

affect reactions through induction.

Infrared (IR) spectroscopy (Section 15.4) In IR, absorption of

IR energy causes bonds to vibrate and rotate.The characteristic

vibrational frequencies can be used to determine the functional

groups present in a molecule.

Inhibitors (Section 11.4) Species that can react with a radical,

thus destroying it. Inhibitors interrupt chain reactions.

Initiation (Section 11.4) The first step in a radical chain reaction

in which a free radical is produced that can start the chain-

carrying or propagation steps.

Integral (Section 15.6) The determination of the relative

numbers of hydrogens corresponding to the signals in an NMR

spectrum.

Inversion of configuration (Section 7.4) The change in the

handedness of a molecule during certain reactions. Generally,

inversion of stereochemistry means that an (R) starting material

would be transformed into an (S) product.

G-10 GLOSSARY

NCO

C O

Ion (Section 1.2) A charged atom or molecule.

Ion-exchange chromatography (Section 23.4) A separation

technique that relies on differences in the affinity of molecules

for a charged substrate.

Ionic bond (Section 1.2) The electrostatic attraction between a

positively charged atom or group of atoms and a negatively

charged atom or group of atoms.

Ionization potential (Section 1.2) A measure of the tendency of

an atom or molecule to lose an electron.

Ipso attack (Section 14.12) Addition to an aromatic ring at a

position already occupied by a nonhydrogen substituent.

Isobutyl group (Section 2.8) The (CH

)

CHCH

group.

Isocyanate (Section 18.14) A compound of the structure

Isoelectric point (pI ) (Section 23.2) The pH at which the amino

acid has no net charge.

Isomers (Section 2.5) Molecules of the same formula but

different structures.

Isoprene (Section 12.13) 2-Methyl-1,3-butadiene.

Isoprene rule (Section 12.13) Most terpenes are composed of

isoprene units combined in “head-to-tail”fashion.

Isopropyl group (Section 2.8) The (CH

)

CH group.

Isotope effect (Section 21.4) The effect on the rate of a reaction

of the replacement of an atom with an isotope.The replacement

of hydrogen with deuterium is especially common.

Karplus curve (Section 15.6) The dependence between the

coupling constant of two hydrogens on adjacent atoms and the

dihedral angle between the carbon–hydrogen bonds.

Kekulé forms (Section 13.3) Resonance forms for benzene in

which overlap between adjacent carbons is emphasized. These

forms superficially resemble 1,3,5-cyclohexatriene.

Ketene (Section 12.3) A compound of the structure

Keto–enol tautomerization (Section 19.2) The equilibrium

between a carbonyl compound and the enol that can be formed if

the carbonyl compound has an α hydrogen.The equilibrium

almost always favors the carbonyl species.

␤-Keto ester or acetoacetate synthesis (Section 19.5) The α

hydrogen between two carbonyl groups can be deprotonated with

weak base.The anion formed will react with an electrophile in

this synthesis.

Ketone (Section 10.5) A compound containing a carbon–oxygen

double bond in which the carbon is attached to two other

carbons.

Ketose (Section 22.2) A sugar containing not the usual aldehyde

group, but a ketone.

Kiliani–Fischer synthesis (Section 22.3) A method of

lengthening the chain of an aldose by one carbon atom. A pair of

sugars, epimeric at the new C(1), is produced.

Kinetic control (Section 8.8) A reaction in which the product

distribution is determined by the heights of the different

transition states leading to products.

Kinetic enolate (Section 19.7) The most easily formed enolate. It

may or may not be the same as the most stable possible enolate,

the thermodynamic enolate.

Kinetic resolution (Section 23.2) A technique for separating a

pair of enantiomers based on the selective transformation of one

of them, often by an enzyme.

Kinetics (Section 8.8) The study of the rates of reactions.

Knoevenagel condensation (Section 19.6) Any of a number of

condensation reactions related to the crossed aldol condensation.

A stabilized anion, often an enolate, is first formed and then adds

to the carbonyl group of another molecule. Dehydration usually

leads to the formation of the final product.

Kolbe electrolysis (Section 17.7) The electrochemical conversion

of carboxylate anions into hydrocarbons. The carboxyl radical

produced loses CO

to give an alkyl radical that dimerizes.

Lactam (Section 17.7) A cyclic amide.

Lactone (Section 17.7) A cyclic ester.

Leaving group (Section 7.3) The departing group in a

substitution or elimination reaction.

Le Châtelier’s principle (Section 8.2) A system at equilibrium

adjusts so as to relieve any stress on it.

Levorotatory (Section 4.4) The rotation of the plane of plane-

polarized light in the counterclockwise direction.

Lewis acid (Section 1.7) Any species that reacts with a Lewis

base. An electrophile.

Lewis base (Section 1.7) Any species with a reactive pair of

electrons. A nucleophile.

Lewis structure (Section 1.3) In a Lewis structure, every electron

(except the 1s electrons for atoms other than hydrogen or helium)

is shown as a dot. In slightly more abstract Lewis structures,

electrons in bonds are shown as lines connecting atoms.

Lithium diisopropylamide (LDA) (Section 19.2) An effective

base for alkylation reactions of carbonyl compounds.This

compound is a strong base but a poor nucleophile, and thus is

effective at removing α hydrogens but not at promoting additions

to carbonyl compounds.

Lobry de Bruijn–Alberda van Ekenstein reaction (Section 22.4)

The base-catalyzed interconversion of aldo and keto sugars.The

key intermediate is the double enol formed by protonation of an

enolate.

Lone-pair electrons (Section 1.3) Electrons in an orbital that is

not involved in binding atoms. See Nonbonding electrons.

Long-range coupling (Section 15.6) Any coupling between

nuclei separated by more than three bonds. It is usually observed

only in high-field

H NMR spectroscopy.

GLOSSARY G-11

LUMO (Section 3.17) Lowest unoccupied molecular orbital.

M + 1 peak (Section 15.3) The signal in a mass spectrum

that comes from a +1 isotope (usually due to

C) of the

molecular ion.

Magid’s second rule (Section 19.11) “Always try the Michael

reaction first.”

Magid’s third rule (Section 19.14) “In times of desperation

and/or despair, when all attempts at solution seem to have failed,

try a hydride shift.”

Malonic ester synthesis (Section 19.5) The alkylation of malonic

esters to produce substituted diesters, followed by hydrolysis and

decarboxylation of the malonic acids to give substituted acetic

acids.

Mannich reaction (Section 19.13) The reaction between a ketone

or aldehyde with an amine to give an imine, which then reacts

with a nucleophile.

Markovnikov’s rule (Section 9.5) In additions of Lewis acids to

alkenes, the Lewis acid will add to the less substituted end of the

alkene.The rule works because additions of Lewis acids in that

way produce the more substituted, more stable carbocation.

Mass spectrometry (MS) (Section 15.3) The analysis of the ions

formed by bombardment of a molecule with high-energy

electrons. High-resolution MS can give the molecular formula of

an ion, and an analysis of the fragmentation pattern can give

information about the structure.

Meerwein–Ponndorf–Verley–Oppenauer (MPVO) equilibration

(Section 19.14) A method of oxidizing alcohols to carbonyl

compounds, or, equivalently, of reducing carbonyls to alcohols,

that uses an aluminum atom to clamp the partners in the reaction

together. A hydride shift is involved in the crucial step.

Meisenheimer complex (Section 14.12) The intermediate in

nucleophilic aromatic substitution formed by the addition of a

nucleophile to an aromatic compound activated by electron-

withdrawing groups, often NO

Mercaptan (Section 6.9) A thiol, RSH.The sulfur counterpart of

an alcohol.

Mercaptide (Section 6.9) The sulfur counterpart of an alkoxide,

Meso compound (Section 4.8) An achiral compound containing

stereogenic atoms.

Messenger RNA (mRNA) (Section 23.5) A polynucleotide

produced from DNA whose base sequence codes for amino acid

assembly.

Meta (Section 13.7) 1,3-Substitution on a benzene ring.

Methane (Section 2.1) The simplest stable hydrocarbon, CH

Methine group (Section 2.8) The CH group.

Methyl anion (Section 2.4)

Methyl cation (Section 2.4)

Methyl compounds (Section 2.3) Substituted methanes,

compounds.

Methylene group (Section 2.7) The CH

group.

Methyl radical (Section 2.4)

Micelle (Section 17.8) An aggregated group of fatty acid salts (or

other molecules) in which a hydrophobic center consisting of the

hydrocarbon chains is protected from an aqueous environment by

a spherical skin of polar hydrophilic groups.

Michael reaction (Section 19.6) The addition of a nucleophile,

often an enolate, to the β position of a double bond of an α,β-

unsaturated carbonyl group.

Microscopic reversibility (Section 8.6) The notion that the

lowest-energy path for a reaction in one direction will also be the

lowest-energy path in the other direction.

Molecular ion (Section 15.3) The charged species obtained by

removing an electron from a molecule.

Molecular orbital (Section 1.1) An orbital not restricted to the

region of space surrounding an atom, but extending over several

atoms in a molecule. Molecular orbitals are formed through the

overlap of atomic or molecular orbitals. Molecular orbitals can be

bonding, nonbonding, or antibonding.

Molozonide (Section 10.5) The initial product of the reaction of

ozone and an alkene.This molecule contains a five-membered

ring with three oxygen atoms in a row. See Primary ozonide.

Monosaccharide (Section 22.6) A simple six-carbon sugar.

Mutarotation (Section 22.4) The interconversion of anomeric

sugars in which an equilibrium mixture of α and β forms is

reached.

n + 1 rule (Section 15.6) The number of lines for a hydrogen will

be n + 1, where n is the number of equivalent adjacent hydrogens.

Natural product (Section 2.12) A product formed in Nature,

which does not include compounds made in the lab.

Neighboring group effect (Section 21.1) A general term for the

influence of an internal nucleophile (very broadly defined) on the

rate of a reaction, or on the structures of the products produced.

Newman projection (Section 2.5) A convention used to draw

what one would see if one could look down a bond.The groups

attached to the front atom are drawn in as three lines. The back

atom is represented as a circle to which its attached bonds are

drawn. Newman projections are enormously useful in seeing

spatial (stereochemical) relationships in molecules.

Ninhydrin (Section 23.3) The hydrate of indan-1,2,3-trione,

a molecule that reacts with amino acids to give the purple dye

used in quantitative analysis of amino acids.

Nitrene (Section 18.14) A reactive intermediate containing a

neutral, monovalent nitrogen atom.The nitrogen counterpart of a

carbene.

Nitrile (Section 18.2) A compound of the structure RCN, also

commonly called a cyanide.

NMR spectrum (Section 2.14) The result of nuclear magnetic

resonance spectroscopy. A spectrum has ppm as the x-axis and

signal intensity as the y-axis.

Node (Section 1.2) The region of zero electron density separating

regions of opposite sign in an orbital. At a node the sign of the

wave function is zero.

Nonbonding electrons (Section 1.3) Electrons in an orbital that

is not involved in binding atoms. See Lone-pair electrons.

Nonbonding orbital (Section 1.5) An orbital that is neither

bonding nor antibonding. An electron in a nonbonding orbital

neither helps to hold the molecule together nor tears it apart.

G-12 GLOSSARY

Nonreducing sugar (Section 22.6) A carbohydrate containing no

amount of an oxidizable aldehyde group.

Norbornyl system (Section 21.3) The bicyclo[2.2.1]heptyl

system.

Nuclear magnetic resonance (NMR) spectroscopy (Section

2.14) Spectroscopy that detects the absorption of energy as the

lower-energy nuclear spin state in which the nuclear spin is

aligned with an applied magnetic field flips to the higher-energy

spin state in which it is aligned against the field. See also

Chemical shift (δ), Coupling constant ( J), and Integral.

Nucleic acid (Section 23.5) The polynucleotides DNA and RNA.

Nucleophile (Section 1.7) A Lewis base. A strong nucleophile

has a high affinity for a carbon 2p orbital.

Nucleophilic aromatic substitution (Section 14.12) The

substitution reaction that occurs when a nucleophile replaces a

group on an aromatic ring, usually a halogen.

Nucleophilicity (Section 7.4) The strength of a nucleophile.

Nucleoside (Section 23.5) A sugar, either ribose or deoxyribose,

bonded to a heterocyclic base at its 1′ position.

Nucleotide (Section 23.5) A phosphorylated nucleoside; one of

the monomers of which DNA and RNA are composed.

Nucleus (Section 1.1) The positively charged core of an atom

containing the protons and neutrons.

Octet rule (Section 1.2) The notion that special stability attends

the filling of the 2s and 2p atomic orbitals to achieve the

electronic configuration of neon, a noble gas.

Off-resonance decoupling (Section 15.7) A technique used in

C NMR in which coupling between

C and

H is restricted to

the hydrogens directly attached to the carbon.The number of

directly attached hydrogens can be determined from the

multiplicity of the observed signal for the carbon.

Olefins (Section 3.8) Hydrocarbons of the general formula,

.These molecules are systematically called alkenes, and

they contain carbon–carbon double bonds.

Optical activity (Section 4.4) The rotation by a molecule of the

plane of plane-polarized light.

Orbital (Section 1.1) A three-dimensional representation of the

solution to the Schrödinger equation. See Wave function (ψ).

Orbital interaction diagram (Section 1.5) A way of analyzing the

interaction between atoms that leads to bonding.

Organocuprate (Section 10.4) An organometallic reagent

CuLi) notable for its ability to react with primary or

secondary halides ( ) to generate hydrocarbons, ,

and to add to the β position of α,β-unsaturated carbonyl

compounds.

Organolithium reagent (Section 6.3) A strongly basic

organometallic reagent, , formed from a halide and

lithium. A characteristic reaction is addition to carbonyl groups.

Organometallic reagent (Section 6.3) Molecule that contains

both carbon and a metal. Usually carbon is at least partially

covalently bonded to the metal. Examples are Grignard reagents,

organolithium reagents, and lithium organocuprates.

Ortho (Section 13.7) 1,2-Disubstituted on a benzene ring.

R¿R¿

Orthogonal orbitals (Section 1.5) Two noninteracting orbitals.

The bonding interactions are exactly balanced by antibonding

interactions.

Osazone (Section 22.4) A 1,2-phenylhydrazone formed by

treatment of a sugar with three equivalents of phenylhydrazine.

Oxaphosphetane (Section 16.17) The four-membered

intermediate in the Wittig reaction that contains two carbons, a

phosphorus, and an oxygen.

Oxirane (Section 7.10) A three-membered ring containing

oxygen, also called an epoxide or oxacyclopropane.

Oxonium ion (Section 3.19) A molecule containing a trivalent,

positively charged, oxygen atom, R

Oxymercuration (Section 10.3) The mercury-catalyzed

conversion of alkenes into alcohols. Addition is in the

Markovnikov sense, and there are no rearrangements. A three-

membered ring containing mercury is an intermediate in the

reaction. Alkynes also undergo oxymercuration to give enols that

are rapidly converted into carbonyl compounds under the

reaction conditions.

Ozonide (Section 10.5) The product of rearrangement of the

primary ozonide formed on reaction of ozone with an alkene.

Ozonolysis (Section 10.5) The reaction of ozone with π systems.

The intermediate products are ozonides that can be transformed

into carbonyl-containing compounds of various kinds.

Paired spin (Section 1.2) Two electrons with opposite spins have

paired spins.

Para (Section 13.7) 1,4-Disubstituted on a benzene ring.

[n]Paracyclophane (Section 14.3) A benzene ring bridged 1,4

(para) with a chain of atoms.

Parallel spin (Section 1.2) Two electrons with the same spin have

parallel spins.These electrons can not occupy the same orbital.

Parent ion (p) (Section 15.3) An ion formed in the mass

spectrometer through loss of a single electron. It can undergo

fragmentation reactions before detection.

Pauli principle (Section 1.2) No two electrons in an atom or

molecule may have the same values of the four quantum

numbers.

Pentose (Section 22.2) A five-carbon sugar.

Peptide (Section 6.1) A polyamino acid in which the constituent

amino acids are linked through amide bonds.They are

distinguished from proteins only by the length of the polymer.

Peptide bond (Section 23.2) The amide bond that links amino

acids.

Ortho esters (Section 17.7) Compounds of the structure

GLOSSARY G-13

Pericyclic reaction (Section 20.1) A reaction in which the

maintenance of bonding overlap between the lobes of the orbitals

involved in bond making and breaking is controlling. All single-

barrier (concerted) reactions can be regarded as pericyclic reactions.

Phenonium ion (Section 21.3) The benzenonium ion produced

through intramolecular displacement of a leaving group by the π

system (not the σ system) of an aromatic ring.

Phenyl (Ph) (Section 13.7) A common and systematic name for

the benzene ring as substituent,

Pi (␲) orbitals (Section 3.2) Molecular orbitals made from the

overlap of p orbitals.

(Section 6.4) The negative logarithm of the acidity constant.

A strong acid has a low pK

, a weak acid has a high pK

Plane-polarized light (Section 4.4) Light that has been passed

through a polarizing filter.

␤-Pleated sheet (Section 23.4) One of the common forms of

secondary peptide structure in which hydrogen bonding holds

chains of amino acids roughly in parallel lines.

Polar covalent bond (Section 1.3) Any shared electron bond

between two different atoms must be polar. Two nonidentical

atoms must have different electronegativities and will attract the

shared electrons to different extents, creating a dipole.

Polarimeter (Section 4.5) A device for measuring the amount of

rotation of the plane of plane-polarized light.

Polyenes (Section 3.4) Any molecule containing multiple double

bonds.

Polynuclear aromatic compound (Section 13.10) An aromatic

molecule composed of two or more fused aromatic rings.

Polysaccharide (Section 22.6) A carbohydrate that is composed

of multiple saccharides.The complex carbohydrates are

polysaccharides.

␣ Position (Section 19.2) The position next to a functional group.

For example, the α position in a ketone is the position adjacent to

the carbon–oxygen double bond.

ppm Scale (Section 15.5) The chemical shift scale commonly

used in NMR spectroscopy in which the positions of absorptions

are quoted as parts per million (ppm) of applied magnetic field.

On the ppm scale, the chemical shift is independent of the

magnetic field.

Primary amine (Section 6.7) An amine bearing only one R group

and two hydrogens.

Primary carbon (Section 2.8) A carbon atom attached to one

other carbon.

Primary ozonide (Section 10.5) The initial product of the

reaction of ozone and an alkene.This molecule contains a five-

membered ring with three oxygen atoms in a row. See

Molozonide.

Primary structure (Section 23.4) The sequence of amino acids in

a protein.

Product-determining step (Section 7.6) The step in a multistep

reaction that determines the structure or structures of the products.

Propagation (Section 11.4) The product-producing steps of a

chain reaction. In the last propagation step, a molecule of product

is formed along with a new radical that can carry the chain.

Propargyl (Section 3.11) The common name for the

group.

Propyl group (Section 2.7) The CH

group.

Protecting group (Section 16.10) Sensitive functional groups in a

molecule can be protected by a reaction that converts them into a

less reactive group, called a protecting group. A protecting group

must be removable to regenerate the original functionality.

Protein (Section 6.1) A polyamino acid in which the constituent

amino acids are linked through amide bonds.They are

distinguished from peptides only through the length of the

polymer.

Protic solvent (Section 6.5) A solvent containing a hydrogen

easily lost as a proton. Examples are water and most alcohols.

Pseudo-first-order reaction (Section 8.4) A bimolecular reaction

in which the concentration of one reagent (usually the solvent)

does not change appreciably.

Pyranose (Section 22.2) A sugar containing a six-membered

cyclic ether.

Pyranoside (Section 22.4) A pyranose in which the anomeric OH

at C(1) has been converted into an OR group.

Pyridine (Section 13.9) Any compound containing the following

“azabenzene” ring system:

Pyrolysis (Section 11.2) The process of inducing chemical change

by supplying heat energy. See Thermolysis.

Pyrrole (Section 13.6) Any compound containing the following

ring structure:

Quantum numbers (Section 1.3) These numbers evolve from the

Schrödinger equation and characterize the various solutions to it.

They may have only certain values, and these values determine

the distance of an electron from the nucleus (n), the shape (l) and

orientation (m

) of the orbitals, and the electron spin (s).

Quaternary carbon (Section 2.8) A carbon attached to four other

carbons.

Quaternary structure (Section 23.4) The structure of a self-

assembled aggregate of two or more protein units.

Racemic mixture (racemate) (Section 4.4) A mixture containing

equal amounts of two enantiomeric forms of a chiral molecule.

Radical anion (Section 10.11) A negatively charged molecule

containing both a pair of electrons and an odd, unpaired electron.

G-14 GLOSSARY

Radical cation (Section 15.3) A species that is positively charged

yet contains a single unpaired electron. These are commonly

formed by ejection of an electron when a molecule is bombarded

with high-energy electrons in a mass spectrometer.

Random coil (Section 23.4) Disordered portions of a chain of

amino acids.

Raney nickel (Section 6.9) A good reducing agent composed of

finely divided nickel on which hydrogen has been adsorbed.

Rate constant (k) (Section 8.5) A fundamental property of a

reaction that depends on the temperature, pressure, and solvent,

but not on the concentrations of the reactants.

Rate-determining step (Section 7.6) The step in a reaction with

the highest-energy transition state.

Reaction mechanism (Section 7.2) Loosely speaking, How does

the reaction occur? How do the reactants come together? Are

there any intermediates? What do the transition states look like?

More precisely, a determination in terms of structure and energy

of the stable molecules, reaction intermediates, and transition

states involved in the reaction, along with a consideration of how

the energy changes as the reaction progresses.

Reactive intermediates (Section 2.4) Molecules of great

instability, and hence fleeting existence under normal conditions.

Most carbon-centered anions, cations, and radicals are examples.

Rearrangement (Section 9.9) The migration of an atom or group

of atoms from one place to another in a molecule.

Rearrangements are exceptionally common in reactions involving

carbocations.

Reducing sugar (Section 22.2) A sugar containing some amount

of an oxidizable free aldehyde group.

Regiochemistry (Section 3.18) The orientation of a reaction

taking place on an unsymmetrical substrate.

Regioselective reaction (Section 7.9) If a reaction may produce

one or more isomers and one predominates, the reaction is called

regioselective.

Resolution (Section 4.9) The separation of a racemic mixture

into its constituent enantiomeric molecules.

Resonance arrow (Section 1.4) A specific way of indicating that

two structures are resonance forms.

Resonance energy (Section 13.5) The energy lowering conferred

by the delocalization of electrons. In benzene, this is the amount

by which benzene is more stable than the hypothetical 1,3,5-

cyclohexatriene containing three localized double bonds. See

Delocalization energy.

Resonance forms (Section 1.4) Many molecules cannot be

represented adequately by a single Lewis form. Instead, two or

more different electronic representations must often be combined

to give a good description of the molecule.These different

representations are called resonance forms.

Retention of configuration (Section 7.4) The preservation of the

handedness of a molecule in a reaction. Generally, retention of

configuration means that an (R) starting material would be

transformed into an (R) product.

Retrosynthetic analysis (Section 16.15) A way of figuring out

how a compound might be synthesized by looking at what

compound was its immediate precursor. This process is applied

step-by-step until readily available starting materials are reached.

Ribonucleic acid (RNA) (Section 23.5) A polymer of nucleotides

made up of ribose units connected by phosphoric acid links. Each

sugar is attached at C(1′) to one of the bases, A, U, G, or C.

Robinson annulation (Section 19.11) A classic method for

construction of six-membered rings using a ketone and methyl

vinyl ketone. It involves a two-step sequence of a Michael

reaction between the enolate of the original ketone and methyl

vinyl ketone, followed by an intramolecular aldol condensation.

Rosenmund reduction (Section 18.6) The reduction of acid

chlorides to aldehydes using a poisoned catalyst and hydrogen.

Ruff degradation (Section 22.3) A method for shortening the

carbon backbone of a sugar by one carbon.The aldehyde carbon

at C(1) is lost and a new aldehyde created at the old C(2).

Saccharide (Section 22.1) A molecule whose formula can be

factored into C

. A sugar or carbohydrate.

Sandmeyer reaction (Section 14.7) The reaction of an aromatic

diazonium ion with cuprous salts to form substituted aromatic

compounds.

Sanger degradation (Section 23.4) A method for determining the

amino acid at the amino terminus of a chain using 2,4-

dinitrofluorobenzene. Unfortunately, the Sanger degradation

hydrolyzes, and thus destroys, the entire peptide.

Saponification (Section 17.8) Base-induced hydrolysis of an

ester, usually a fatty acid.

Saturated hydrocarbons (Section 2.12) Alkanes of the molecular

formula C

2n + 2

Saytzeff elimination (Section 7.8) Formation of the more

substituted alkene in an elimination reaction.

Schiff base (Section 16.11) The nitrogen analogue of a ketone or

aldehyde. See Imine.

Secondary amine (Section 6.7) An amine bearing one hydrogen

and two R groups.

Secondary carbon (Section 2.8) A carbon attached to two other

carbons.

Secondary structure (Section 23.4) Ordered regions of a protein

chain.The two most common types of secondary structure are

the α-helix and the β-pleated sheet.

Second-order reaction (Section 8.4) A reaction for which the

rate depends on the product of a rate constant and the

concentrations of two reagents.

Side chain (Section 23.2) The group attached to the α carbon of

an amino acid.

Sigma bond (Section 2.2) Any bond with cylindrical symmetry.

Sigmatropic shift (Section 20.5) The migration of an atom or

group, under orbital symmetry control, along a π system.

Silyl ether (Section 16.10) A molecule of the general form

R—O—SiR

Singlet carbene (Section 10.4) A singlet carbene contains only

paired electrons. In a singlet carbene, the two nonbonding

electrons have opposite spins and occupy the same orbital.

1 Reaction (Section 7.6) Substitution, nucleophilic,

unimolecular. An initial ionization is followed by attack of the

nucleophilic solvent.

2 Reaction (Section 7.4) Substitution, nucleophilic,

bimolecular. In this reaction, the nucleophile dispaces the leaving

–

GLOSSARY

G-15

–

R+

–

R+

group by attack from the rear.The stereochemistry of the starting

material is inverted.

Soap (Section 17.8) The sodium salt of a fatty acid.

Solvated electron (Section 10.11) The species formed when

sodium is dissolved in ammonia.The product is a sodium ion and

an electron surrounded by ammonia molecules. This electron can

add to alkynes (and some other π systems) in a reduction step.

Solvation (Section 6.4) The stabilizing effects of a solvent,

typically the stabilization of ions by a polar solvent.

Solvolysis reaction (Section 7.6) In such S

1 and S

2 reactions,

the solvent acts as the nucleophile.

Specific rotation (Section 4.5) The rotation of plane-polarized

light induced by a solution of a molecule of concentration

1 g/mL in a tube 10 cm long.

Spectroscopy (Section 2.14) The study of the interactions

between electromagnetic radiation and atoms and molecules.

sp Hybrid (Section 2.2) A hybrid orbital made by the

combination of one s and one p atomic orbital.

Hybrid (Section 2.2) A hybrid orbital made by the

combination of one s orbital and two p orbitals.

Hybrid (Section 2.2) A hybrid orbital made by the

combination of one s orbital and three p orbitals.

Spiro (Section 5.7) A structural motif in which two rings share a

single carbon.

Staggered ethane (Section 2.5) The energy minimum

conformation of ethane in which the carbon–hydrogen bonds

(and the electrons in them) are as far apart as possible.

Starch (Section 22.6) A nonlinear polymer of glucose containing

amylose, an α-linked linear polymer of glucose.

Stereochemistry (Section 4.1) The physical and chemical

consequences of the arrangement in space of the atoms in

molecules.

Stereogenic atom (Section 4.3) An atom, usually carbon, of such

nature and bearing groups of such nature that it can have two

nonequivalent configurations.

Steric requirements (Section 2.9) The space required by an atom

or group of atoms.

Steroid (Section 12.14) A class of four-ring compounds, always

containing three six-membered rings and one five-membered

ring.The ring system can be substituted in many ways, but the

rings are always connected in the following fashion:

Strecker synthesis (Section 23.2) A synthesis of amino acids

using an aldehyde, cyanide, and ammonia, followed by hydrolysis.

Structural isomers (Section 2.7) Molecules of the same formula

that differ structurally.

Substituent (Section 2.3) Any atom or group of atoms other than

hydrogen attached to a molecule.

Substitution reaction (Section 7.1) The replacement of a leaving

group in by a nucleophile, Nu

.Typically,

Sugar (Section 22.1) A molecule whose formula can be factored

into C

. A saccharide or carbohydrate.

Sulfide (Section 6.9) The sulfur counterpart of an ether, RSR′.

See Thioether.

Sulfone (Section 16.16) , the final product of

oxidation of a sulfide with hydrogen peroxide.

Sulfonium ion (Section 7.10) A positively charged sulfur ion,

Sulfoxide (Section 16.16) A compound of the structure

Superacid (Section 14.13) A number of highly polar, highly

acidic, but weakly or nonnucleophilic solvent systems. Superacids

are often useful in stabilizing carbocations, at least at low

temperature.

Suprafacial motion (Section 20.5) Migration of a group in a

sigmatropic shift in which bond breaking and bond making take

place on the same side of the π system.

syn Addition (Section 9.10) The addition of two groups to a π

bond in which the two groups end up being on the same side.

syn Elimination (Section 7.9) An elimination reaction in which

the dihedral angle between the breaking bonds, usually

, is 0°.

Tautomerization (Section 10.8) The process through which

molecules related through the change of position of a single

hydrogen interconvert.

Tautomers (Section 1.4) Molecules related through the change of

position of a single hydrogen.

Termination (Section 11.4) The mutual annihilation of two

radicals. Termination steps destroy chain-carrying radicals and

end chains through bond formation.

Terpenes (Section 12.13) Compounds whose carbon skeletons

are composed of isoprene units.

Tertiary amine (Section 6.7) An amine bearing no hydrogens and

three R groups.

Tertiary carbon (Section 2.8) A carbon attached to three other

carbons.

Tertiary structure (Section 23.4) The structure of a protein

induced by its folding pattern.

Tetrahedral intermediate (Section 17.7) The first intermediate

formed when a nucleophile attacks a carbonyl carbon.

Tetrahydropyranyl (THP) ether (Section 16.10) Protecting

groups for alcohols of the structure

H and C

G-16 GLOSSARY

RHN

NHR

....

Tetramethylsilane (TMS) (Section 15.5) The standard “zero

point” on the ppm scale in NMR spectroscopy. The chemical

shift of a nucleus is quoted in parts per million of applied

magnetic field relative to the position of TMS.

Te t ro s e (Section 22.2) A four-carbon sugar.

Thermodynamic control (Section 8.8) In a reaction under

thermodynamic control, the product distribution depends on the

energy differences between the products.

Thermodynamic enolate (Section 19.15) The most stable

enolate. It may or may not be the same as the most rapidly

formed enolate, the kinetic enolate.

Thermodynamics (Section 8.8) The study of energetic

relationships.

Thermolysis (Section 11.2) The process of inducing chemical

change by supplying heat energy. See Pyrolysis.

Thioether (Section 6.9) The sulfur counterpart of an ether, RSR′.

A sulfide.

Thiol (Section 6.9) The sulfur counterpart of an alcohol, RSH.

Thionyl chloride (Section 7.4) SOCl

, an effective reagent for

converting alcohols into chlorides and carboxylic acids into acid

chlorides.

Thiourea (Section 23.4) A compound of the structure

Three-center, two-electron bonding (Section 21.3) A bonding

system in which only two electrons bind three atoms.This

arrangement is common in electron-deficient molecules such as

boranes and carbocations.

Torsional strain (Section 5.2) Destabilization caused by the

proximity of bonds (usually eclipsing) and the electrons in them.

trans (Section 2.12) Hydrogens on opposite sides. Used to specify

stereochemical (spatial) relationships in ring compounds and

alkenes.

s-trans (Section 12.6) The more stable, extended form of a

1,3-diene:

Transesterification (Section 18.8) The formation of one ester

from another. The reaction can be catalyzed by either acid or

base.

Transition state (TS) (Section 2.5) The high point in energy

between starting material and product. The transition state is an

energy maximum and not an isolable compound.

Triple bond (Section 3.5) Two atoms can be attached by a triple

bond composed of one σ bond and two π bonds.

Triplet carbene (Section 10.4) In a triplet carbene, the two

nonbonding electrons have the same spin and must occupy

different orbitals.

Tropylium ion (Section 13.6) The 1,3,5-cycloheptatrienylium

ion.This ion has 4n + 2 π electrons (n = 1) and is aromatic.

Ultraviolet/visible (UV/vis) spectroscopy (Section 12.7)

Electronic spectroscopy using light of wavelength 200–400 nm.

Unpaired spin (Section 1.2) Two electrons with the same spin

quantum number have unpaired spin.

Unsaturated hydrocarbons (Section 2.12) Molecules containing

π bonds. For example, alkenes or alkynes. This term does not

include cycloalkanes.

Urea (Section 17.7)

Valence electrons (Section 1.3) The outermost, or most loosely

held, electrons.

van der Waals forces (Section 2.13) Attractive or repulsive

intermolecular forces in or between molecules caused by induced

dipole–induced dipole interactions.

van der Waals strain (Section 5.4) Repulsive forces in or between

molecules caused by induced dipole–dipole interactions.

Vicinal (Section 10.2) Groups on adjacent carbons are vicinal.

Vinyl (Section 3.3) The common name for the

group.

Vinylic hydrogen (Section 15.6) A hydrogen on an alkene.

Wagner–Meerwein rearrangement (Section 9.9) The 1,2-

migration of an alkyl group in a carbocation.

Wave function (ψ) (Section 1.2) A solution to the Schrödinger

equation, another word for orbital.

Wavenumber (Section 15.4) The wavenumber (ν

−

) equals 1/λ

or ν/c.

Weighting factor (Section 1.4) The relative contribution of a

particular resonance structure to the weighted sum of all

resonance forms.

Williamson ether synthesis (Section 7.10) The S

2 reaction of

an alkoxide with to give an ether.

Wittig reaction (Section 16.17) The reaction of an ylide with a

carbonyl group to give, ultimately, an alkene.

Wolff rearrangement (Section 18.14) The formation of a ketene

through the thermal or photochemical decomposition of a diazo

ketone.

Woodward–Hoffmann theory (Section 20.1) The notion that

one must take account of the phase relationships between orbitals

in order to understand reaction mechanisms. In a concerted

reaction, bonding relationships must be maintained at all times.

Xanthate ester (Section 18.13) A compound of the structure

Ylide (Section 16.17) A compound containing opposite charges

on adjacent atoms.

Zwitterion (Section 23.2) A dipolar species in which full plus and

minus charges coexist within the same molecule.

Credits

C-1

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CHAPTER 2

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CHAPTER 5

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CHAPTER 9

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Fundamental Photographs.

CHAPTER 10

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CHAPTER 11

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CHAPTER 12

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CHAPTER 19

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AGES/Brand X/Alamy.

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CHAPTER 23

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