Glossary – Advanced Organic Chemistry

Glossary

absolute configuration the three-dimensional structure of a chiral compound. The configuration is designated by R or S.
absorption band a peak in a spectrum that occurs as a result of absorption of energy.
acetal
acetoacetic ester synthesis synthesis of a methyl ketone using ethyl acetoacetate as the starting material.
achiral (optically inactive) an achiral molecule has a superimposable mirror image and does not rotate the plane of polarized light.
acid a substance that donates a proton or accepts a pair of electrons.
acid anhydride
acid-base reaction a reaction in which an acid donates a proton to a base.
acid catalyst a catalyst that increases the rate of a reaction by donating a proton.
acid-catalyzed reaction a reaction catalyzed by an acid.
acid dissociation constant a measure of the degree to which an acid dissociates.
activating substituent a substituent that increases the reactivity of an aromatic ring. Electron-donating substituents activate aromatic rings toward electrophilic attack, and electron-withdrawing substituents activate aromatic rings toward nucleophilic attack.
activation energy the miminmum energy which reacting species must possess in order to be able to form an ‘activated complex’, or ‘transition state’, before proceeding to the products. [The activation energy (Ea) may be derived from the temperature dependence of the reaction rate using the Arrhenius equation].
active site a pocket or cleft in an enzyme where the substrate is bound.
acyclic noncyclic
acyl group a carbonyl group bonded to an alkyl group or to an aryl group.
acyl halide
1,2-addition (direct addition) addition to the 1- and 2-positions of a conjugated system.
1,4-addition (conjugate addition) addition to the 1- and 4-positions of a conjugated system.
addition polymer (chain-growth polymer) made by adding monomers to the growing end of a chain.
addition reaction a reaction in which atoms or groups are added to the reactant.
alcohol (ROH) a compound with an OH group in place of one of the hydrogens of an alkane.
alcoholysis reaction with alcohol
aldaric acid a dicarboxylic acid with an OH group bonded to each carbon. Obtained by oxidizing the aldehyde and primary alcohol groups of an aldose.
aldehyde
alditol a compound with an OH group bonded to each carbon. Obtained by reducing an aldose or a ketose.
aldol addition a reaction between two molecules of an aldehyde (or two molecules of a ketone) that connects the α-carbon of one with the carbonyl carbon of the other.
aldol condensation an aldol addition followed by elimination of water.
aldonic acid a carboxylic acid with an OH group bonded to each carbon. Obtained by oxidizing the aldehyde group of an aldose.
aldose a polyhydroxyaldehyde.
aliphatic compound a non-aromatic organic compound.
alkaloid a natural product with one or more nitrogen hetero atoms found in the leaves, bark, or seeds of plants.
alkane a hydrocarbon that contains only single bonds.
alkene a hydrocarbon that contains a double bond.
alkoxymercuration addition of alcohol using a mercuric salt of a carboxylic acid as a catalyst.
alkylation reaction a reaction that adds an alkyl group to a reactant.
alkyl halide a compound with a halogen in place of one of the hydrogens of an alkane.
alkyl substituent (alkyl group) formed by removing a hydrogen from an alkane.
alkyl tosylate an ester of para-toluenesulphonic acid.
alkyne a hydrocarbon that contains a triple bond.
allene a compound with two adjacent double bonds.
allyl group CH2=CHCH2
allylic carbon an sp3 carbon adjacent to a vinyl carbon.
allylic cation a compound with a positive charge on an allylic carbon
.
alpha olefin a monosubstituted olefin.
alternating copolymer a copolymer in which two monomers alternate.
ambident nucleophile a nucleophile with two nucleophilic sites.
amide
amine a compound with a nitrogen in place of one of the hydrogens of an alkane (RNH2, R2NH, R3N).
amine inversion a compound containing an sp3 hybridized nitrogen with a nonbonding pair of electrons that rapidly turns inside out.
amino acid an α-aminocarboxylic acid. Naturally occurring amino acids have the L configuration.
aminolysis reaction with an amine.
amino sugar a sugar in which one of the OH groups is replaced by an NH2 group.
amphoteric compound a compound that can behave either as an acid or as a base.
anchimeric assistance (intramolecular catalysis) catalysis in which the catalyst that facilitates the reaction is part of the molecule undergoing reaction.
angle strain the strain introduced into a molecule as a result of its bond angles being distorted from their ideal values.
angular methyl group a methyl substituent at the 10- or 13-position of a steroid ring system.
anion-exchange resin a positively charged resin used in ion exchange chromatography.
anionic polymerization chain-growth polymerization in which the initiator is a nucleophile; the propagation site therefore is an anion.
annulation reaction a ring-forming reaction.
annulene a monocyclic hydrocarbon with alternating double and single bonds.
anomeric carbon the carbon in a cyclic sugar that is the carbonyl carbon in the open-chain form.
anomeric effect the preference for the axial position shown by certain substituents bonded to the anomeric carbon of a six-member ring sugar.
anomers the specific term used to describe carbohydrate stereoisomers differing only in configuration at the hemi-acetal carbon atom, that is, two cyclic sugars that differ in configuration only at the carbon, that is, the carbonyl carbon in the open-chain form.
antarafacial bond formation formation of two σ bonds from opposites sides of the π system.
antarafacial rearrangement rearrangement in which the migrating group moves to the opposite face of the π system.
anti addition an addition reaction in which the two added subtituents add to opposite sides of the molecule.
anti-aromatic a cyclic and planar compound with an uninterrupted ring of π orbital-bearing atoms containing an even number of pairs of π electrons.
antibiotic a compound that interferes with the growth of a microorganism.
antibodies compounds that recognize foreign particles in the body.
antibonding molecular orbital a molecular orbital that results when two atomic orbitals with opposite signs interact. Electrons in an antionding orbital decrease bond strength.
anti conformer the most stable of the staggered conformers.
anti elimination an elimination reaction in which the two subituents eliminated are removed from opposite sides of the molecule.
anti-periplanar parallel substituents on opposite sides of a molecule.
antiviral drug a drug that interferes with DNA or RNA synthesis in order to prevent a virus from replicating.
applied magnetic field the externally applied magnetic field.
aprotic solvent a solvent that does not have a hydrogen bonded to an oxygen or to a nitrogen.
arene oxide an aromatic compound that has had one of its double bonds converted to an epoxide.
aromatic a cyclic and planar compound with an uninterrupted ring of π orbital-bearing atoms containing an odd number of pairs of π electrons. An aromatic molecule or ion possesses aromaticity. Aromaticity is the special property of planar (or nearly planar) cyclic, conjugated systems having (4n+2) conjugated π (pi) electrons. The delocalization of the (4n+2) π (pi) electrons gives them special stability. For benzene, the most common aromatic system (n = 1, therefore 6 π (pi) electrons), the aromaticity confers the characteristic reactivity of electrophilic substitution.
aroyl group a carbonyl group attached to an aromatic ring.
Arrhenius equation relates the rate constant of a reaction to the energy of activation and to the temperature at which the reaction is carried out (k + Ae−Ea/RT).
asymmetrical ether an ether with two different substituents bonded to the oxygen.
asymmetric molecular orbital a molecular orbital in which the left half is not a mirror of the right half.
atomic number tells how many protons (or electrons) the neutral atom has.
atomic orbital an orbital associated with an atom.
atomic weight the average mass of the atoms in the naturally occurring element.
aufbau principle states that an electron will always go into the available orbital with the lowest energy.
auxochrome a substituent that, when attached to a chromophore, alters the λmax and intensity of absorption of ultraviolet/visible radiation.
Avogadro’s constant the number of particles (atoms or molecules) in one mole of any pure substance. [6.023 × 1023]
axial bond a bond of the chair form of cyclohexane that is perpendicular to the plane in which the chair is drawn (an up-down bond).
aziridine a three-member ring compound in which one of the ring atoms is a nitrogen.
azo linkage a -N=N- bond.
back side attack nucleophilic attack on the side of the carbon opposite to the side bonded to the leaving group.
bactericidal drug a drug that kills bacteria.
bacteriostatic drug a drug that inhibits the further growth of bacteria.
Baeyer-Villiger oxidation oxidation of aldehydes or ketones with H2O2 or peracids to form carboxylic acids or esters, respectively.
banana bond the σ bonds in small rings that are weaker as a result of overlapping at an angle rather than overlapping head-on.
base1 a substance that accepts a proton or donates a pair of electrons.
base2 a heterocyclic compound (a purine or a pyrimidine) in DNA and RNA.
base catalyst a catalyst that increases the rate of a reaction by removing a proton.
basicity describes the tendency of a compound to share its electrons with a proton.
Beer-Lambert law relationship among the absorbance of UV/Vis light: the concentration of the sample, the length of the light path, find the molar absorptivity.
bending vibration a vibration that does not occur along the line of the bond.
benzoyl group a benzene ring bonded to a carbonyl group.
benzylic carbon an sp3 hybridized carbon bonded to a benzene ring.
benzylic cation a compound with a positive charge on a benzylic carbon.
benzyl group
benzyne intermediate a compound with a triple bond in place of one of the double bonds of benzene.
bicyclic compound a compound that contains two rings that share at least one carbon.
bifunctional molecule a molecule with two functional groups.
bimolecular reaction (second-order reaction) a reaction whose rate is dependent on the concentration of two reactants.
biochemistry (biological chemistry) the chemistry of biological systems.
bioorganic compound an organic compound that is found in biological systems.
biosynthesis synthesis in a biological system.
Birch reduction the partial reduction of benzene to 1,4-cyclohexadiene.
block copolymer a copolymer in which there are blocks of each kind of monomer.
blue shift a shift to a shorter wavelength.
boat conformation the conformation of cyclohexane that roughly resembles a boat.
boiling point the temperature at which a liquid vapourizes.
bonding molecular orbital a molecular orbital that results when two atomic orbitals with the same sign interact. Electrons in a bonding orbital increase bond strength.
bond length the internuclear distance between two atoms at minimum energy (maximum stability).
brand name (proprietary name, trade name) identifies a commercial product and distinguishes it from other products. Only the owner of the registered trademark can use it.
bridged bicyclic compound a bicyclic compound in which rings share two nonadjacent carbons.
Bronsted acid a substance that donates a proton.
Bronsted base a substance that accepts a proton.
buffer an acid and its conjugate base.
carbanion a compound containing a negatively charged carbon.
Carbene a species with a carbon that has a nonbonded pair of electrons and an empty orbital (H2C:).
carbocation a compound containing a positively charged carbon.
carbocation rearrangement the rearrangement of a carbocation to a more stable carbocation.
carbohydrate a sugar, a saccharide. Naturally occurring carbohydrates have the D configuration.
α-carbon a carbon adjacent to a carbonyl carbon.
carbon acid a compound that contains a carbon that is bonded to a relatively acidic hydrogen.
carbonyl addition (direct addition) nucleophilic addition to the carbonyl carbon.
carbonyl carbon the carbon of a carbonyl group.
carbonyl compound a compound that contains a carbonyl group.
carbonyl group a carbon doubly bonded to an oxygen.
carbonyl oxygen the oxygen of a carbonyl group.
carboxyl group COOH
carboxylic acid R-COOH
carboxylic acid derivative a compound that is hydrolyzed to a carboxylic acid.
carboxyl oxygen the singly bonded oxygen of a carboxylic acid or an ester.
catalyst a species that increases the rate at which a reaction occurs without being consumed in the reaction. Because it does not change the equilibrium constant of the reaction, it does not change the amount of product that is formed.
catalytic hydrogenation the addition of hydrogen to a double or a triple bond with the aid of a metal catalyst.
chair conformation the conformation of cyclohexane that roughly resembles a chair. It is the most stable conformation of cyclohexane.
chemical exchange the transfer of a proton from one molecule to another.
chemically equivalent protons protons with the same connectivity relationship to the rest of the molecule.
chemical shift the location of a signal in an NMR spectrum. It is measured downfield from a reference compound (most often TMS).
chichibabin reaction the reaction of pyridine with sodium amide to form 2-aminopyridine (and some 4-aminopyridine).
chiral (optically active) a chiral molecule has a non-superimposable mirror image.
chiral auxiliary an enantiomerically pure compound which, when attached to a reactant, causes a product with particular configuration to be formed.
chirality centre an atom bonded to four different groups.
cholesterol a steroid that is the precursor of all other steroids.
chromatography a separation technique in which the mixture to be separated is dissolved in a solvent and the solvent passed through a column packed with an adsorbent stationary phase. A series of related techniques exist for the separation of a mixture of compounds by their distribution between two phases. In gas-liquid chromatography the distribution is between a gaseous and a liquid phase. In column chromatography the distribution is between a liquid and a solid phase.
chromophore the part of a molecule responsible for a ultraviolet or visible spectrum.
cine substitution substitution at the carbon adjacent to the carbon that was bonded to the leaving group.
cis fused two cyclohexane rings fused together such that, if the second ring were considered to be two substituents of the first ring, one substituent would be in an axial position and the other would be in an equatorial position.
cis isomer the isomer with identical substituents on the same side of the double bond.
cis-trans isomers geometric isomers.
Claisen condensation a reaction between two molecules of an ester that connects the α-carbon of one with the carbonyl carbon of the other and eliminates an alkoxide ion.
Claisen rearrangement a [3,3] sigmatropic rearrangement of an allyl vinyl ether.
α-cleavage homolytic cleavage of an alpha substituent.
Clemmensen reduction a reaction that reduces the carbonyl group of a ketone to a methylene group using Zn(Hg)/HCI.
combination band occurs at the sum of two fundamental absorption frequencies (v1 + v2).
combinatorial library a group of structurally related compounds.
combinatorial organic synthesis the synthesis of a library of compounds by covalently connecting sets of building blocks of varying structure.
common intermediate an intermediate that two compounds have in common.
common name nonsystematic nomenclature.
competitive inhibitor a compound that inhibits an enzyme by competing with the substrate for binding at the active site.
complete racemization formation of a pair of enantiomers in equal amounts.
complex carbohydrate contains two or more sugar molecules linked together.
concerted reaction a reaction in which all the bond-making and bond-breaking processes occur in one step.
condensation polymer (step-growth polymer) made by combining two molecules while removing a small molecule (usually water or an alcohol).
condensation reaction a reaction combining two molecules while removing a small molecule (usually water or an alcohol).
conducting polymer a polymer that can conduct electricity down its backbone.
configuration the three-dimensional structure of a chiral compound. The configuration is designated by R or S.
configurational isomers stereoisomers that cannot interconvert unless a covalent bond is broken. Cis-trans isomers and optical isomers are configurational isomers.
conformation the three-dimensional shape of a molecule at a given instant.
conformational analysis the investigation of the various conformations of a compound and their relative stabilities.
conformers (conformational isomers) different conformations of a molecule.
conjugate acid a compound accepts a proton to form its conjugate acid.
conjugate base a compound loses a proton to form its conjugate base.
conjugated double bonds double bonds separated by one single bond.
conrotatory ring closure achieves head-to-head overlap of π orbitals by rotating the orbitals in the same direction.
conservation of orbital symmetry theory a theory that explains the relationship between the structure and configuration of the reactant, the conditions under which a pericyclic reaction takes place, and the configuration of the product.
constitution the number and type of atoms in a molecule.
constitutional isomers (structural isomers) molecules that have the same molecular formula but differ in the way the atoms are connected.
contributing resonance structure a structure with localized electrons that approximates the true structure of a compound with delocalized electrons.
convergent synthesis a synthesis in which pieces of the target compound are individually prepared and then assembled.
Cope elimination reaction elimination of a proton and a hydroxylamine from an amine oxide.
Cope rearrangement a [3,3] sigmatropic rearrangement of a 1,5-diene.
copolymer a polymer formed using two or more different monomers.
corrin ring system a porphyrin ring system without one of the methine bridges.
COSY spectrum A 2-D NMR spectrum that shows coupling between sets of protons.
coupled protons protons that split each other. Coupled protons have the same coupling constant.
coupling constant the distance (in hertz) between two adjacent peaks of a split NMR signal.
coupling reaction a reaction that joins two alkyl groups.
covalent bond a bond created as a result of sharing electrons.
covalent catalysis (nucleophilic catalysis) catalysis that occurs as a result of a nucleophile forming a covalent bond with one of the reactants.
Cram’s rule the rule used to determine the major product of a carbonyl addition reaction in a compound with a chirality centre adjacent to the carbonyl group.
cross-conjugation nonlinear conjugation.
crossed (mixed) aldol addition an aldol addition in which two different carbonyl compounds are used.
cross-linking connecting polymer chains by intermolecular bond formation.
crown ether a cyclic molecule that contains several ether linkages.
crown-guest complex the complex formed when a crown ether binds a substrate.
cryptand a three-dimensional polycyclic compound that binds a substrate by encompassing it.
cryptate the complex formed when a cryptand binds a substrate.
crystallites regions of a polymer in which the chains are highly ordered.
cumulated double bonds double bonds that are adjacent to one other.
Curtius rearrangement conversion of an acyl chloride into a primary amine using N3.
cyanohydrin
cycloaddition reaction a reaction in which two π-bond-containing molecules react to form a cyclic compound.
[4 + 2] cycloaddition reaction a cycloaddition reaction in which 4 π electrons come from one reactant and 2 π electrons come from the other reactant.
cycloalkane an alkane with its carbon chain arranged in a closed ring.
deactivating substituent a substituent that decreases the reactivity of an aromatic ring. Electron-withdrawing substituents deactivate aromatic rings towards electrophilic attack, and electron-donating substituents deactivate aromatic rings towards nucleophilic attack.
deamination loss of ammonia.
decarboxylation loss of carbon dioxide.
degenerate orbitals orbitals that have the same energy.
dehydration loss of water.
dehydrohalogenation elimination of a proton and a halide ion.
delocalization energy (resonance energy) the extra stability a compound achieves as a result of having delocalized electrons.
delocalized electrons electrons that are shared by more than two atoms.
deoxygenation removal of an oxygen from a reactant.
deoxyribonucleic acid (DNA) a polymer of deoxyribonucleotides.
deoxyribonucleotide a nucleotide in which the sugar component is D-2-deoxyribose.
deoxy sugar a sugar in which one of the OH groups has been replaced by an H.
DEPT 13C NMR spectrum a series of four spectra that distinguishes among −CH3, −CH2 and −CH groups.
detergent a salt of a sulphonic acid.
deuterium kinetic isotope effect ratio of the rate constant obtained for a compound containing hydrogen and the rate constant obtained for an identical compound in which one or more of the hydrogens have been replaced by deuterium.
dextrorotatory the enantiomer that rotates polarized light in a clockwise direction.
diastereomer a configurational isomer that is not an enantiomer.
diastereotopic hydrogens two hydrogens bonded to a carbon that, when replaced in turn with a deuterium, results in a pair of diastereomers.
1,3-diaxial interaction the interaction between an axial substituent and the other two axial substituents on the same side of the cyclohexane ring.
diazonium ion ArN2+ or RN2+
diazonium salt a diazonium ion and an anion ArN2+X.
Dieckmann condensation an intramolecular Claisen condensation.
dielectric constant a measure of how well a solvent can insulate opposite charges from one another.
Diels-Alder reaction a [4 + 2] cycloaddition reaction.
diene a hydrocarbon with two double bonds.
dienophile an alkene that reacts with a diene in a Diels-Alder reaction.
dihedral angle the angle between groups attached on adjacent carbon atoms when viewed in a Newmann projection.
β-diketone a ketone with a second carbonyl group at the β-position.
dimer a molecule formed by the joining together of two identical molecules.
Dipole–dipole interaction an interaction between the dipole of one molecule and the dipole of another.
dipole moment (μ) a measure of the separation of charge in a bond or in a molecule.
direct displacement mechanism a reaction in which a nucleophile displaces the leaving group in a single step.
direct substitution substitution at the carbon that was bonded to the leaving group.
disaccharide a compound containing two sugar molecules linked together.
disconnection breaking a bond to carbon to give a simpler species.
disproportionation transfer of a hydrogen atom by a radical to another radical with the result that an alkane and an alkene are formed.
disrotatory ring closure achieves head-to-head overlap of p orbitals by rotating the orbitals in opposite directions.
dissociation energy the amount of energy required to break a bond/the amount of energy released when a bond is formed.
dissolving metal reduction a reduction using sodium or lithium metal dissolved in liquid ammonia.
disulphide bridge a disulphide (-S-S-) bond in a peptide or protein.
DNA (deoxyribonucleic acid) a polymer of deoxyribonucleotides.
double bond a sigma bond and a pi bond.
doublet an NMR signal split into two peaks.
doublet of doublets an NMR signal split into four peaks of approximately equal height. Caused by splitting a signal into a doublet by one hydrogen and into another doublet by another (nonequivalent) hydrogen.
drug a compound that reacts with a biological molecule, triggering a physiological effect.
eclipsed conformation a conformation in which the bonds on adjacent carbons are parallel to each other as viewed looking down the carbon–carbon bond.
E conformation the conformation of a carboxylic acid or carboxylic acid derivative in which the carbonyl oxygen and the substituent bonded to the carboxyl oxygen or nitrogen are on opposite sides of the single bond.
Edman’s reagent phenyl isothiocyanate. A reagent used to determine the N-terminal amino acid of a polypeptide.
effective magnetic field the magnetic field that a proton ‘senses’ through the surrounding cloud of electrons.
effective molarity the concentration of the reagent that would be required in an intermolecular reaction for it to have the same rate as an intramolecular reaction.
E isomer the isomer with the high-priority groups on opposite sides of the double bond.
elastomer a polymer that can stretch and then revert back to its original shape.
electrocyclic reaction a reaction in which a π bond in the reactant is lost so that a cyclic compound with a new σ bond can be formed.
electromagnetic radiation radiant energy that displays wave properties.
electron affinity the energy given off when an atom acquires an electron.
electronegative describes an element that readily acquires an electron.
electronegativity tendency of an atom to pull electrons toward itself.
electronic transition promotion of an electron from its HOMO to its LUMO.
electron sink site to which electrons can be delocalized.
electrophile an electron-deficient atom or molecule.
electrophilic addition reaction an addition reaction in which the first species that adds to the reactant is an electrophile.
electrophilic aromatic substitution a reaction in which an electrophile substitutes for a hydrogen of an aromatic ring.
electrophilic catalysis catalysis in which the species that facilitates the reaction is an electrophile.
electropositive describes an element that readily loses an electron.
electrostatic attraction attractive force between opposite charges.
elemental analysis a determination of the relative proportions of the elements present in a compound.
α-elimination removal of two atoms or groups from the same carbon.
β-elimination removal of two atoms or groups from adjacent carbons.
E1 reaction a first-order elimination reaction.
E2 reaction a second-order elimination reaction.
elimination reaction a reaction that involves the elimination of atoms (or molecules) from the reactant.
empirical formula the relative numbers of the different kinds of atoms in a molecule.
enamine an α,β-unsaturated tertiary amine.
enantiomerically pure containing only one enantiomer.
enantiomeric excess (optical purity) how much excess of one enantiomer is present in a mixture of a pair of enantiomers.
enantiomers non-superimposable mirror-image molecules.
enantioselective reaction a reaction that forms an excess of one enantiomer.
enantiotopic hydrogens two hydrogens bonded to a carbon that is bonded to two other groups that are nonidentical.
endergonic reaction a reaction with a positive ΔG°.
endo a substituent is endo if it is closer to the longer or more unsaturated bridge.
endothermic reaction a reaction with a positive ΔH°.
enolization keto-enol interconversion.
enthalpy the heat given off (−ΔH°) or the heat absorbed (+ΔH°) during the course of a reaction.
entropy a measure of the freedom of motion in a system.
enzyme a protein that is a catalyst.
epimerization changing the configuration at a chirality centre by removing a proton from it and then reprotonating the molecule at the same site.
epimers monosaccharides that differ in configuration at only one carbon.
epoxidation formation of an epoxide.
equatorial bond a bond of the chair form of cyclohexane that juts out from the ring in approximately the same plane that contains the chair.
equilibrium constant the ratio of products to reactants at equilibrium or the ratio of the rate constants for the forward and reverse reactions.
equilibrium control thermodynamic control.
erythro enantiomers the pair of enantiomers with similar groups on the same side when drawn in a Fischer projection.
essential amino acid an amino acid that humans must obtain from their diet because they cannot synthesize it or cannot synthesize it in adequate amounts.
ether a compound containing an oxygen bonded to two carbons (ROR).
excited-state electronic configuration the electronic configuration that results when an electron in the ground-state electronic configuration has been moved to a higher-energy orbital.
exergonic reaction a reaction with a negative ΔG°.
exhaustive methylation reaction of an amine with excess methyl iodide resulting in the formation of a quaternary ammonium iodide.
exo a substituent is exo if it is closer to the shorter or more saturated bridge.
exothermic reaction a reaction with a negative ΔH°.
experimental energy of activation (Ea = ΔH# - RT*) a measure of the approximate energy barrier to a reaction. (It is approximate because it does not contain an entropy component).
extrusion reaction a reaction in which a neutral molecule (for example, CO2, CO, or N2) is eliminated from a molecule.
fat a triester of glycerol that exists as a solid at room temperature.
fatty acid a long-chain carboxylic acid.
fingerprint region the right-hand third of an infrared spectrum where the absorption bands are characteristic of the compound as a whole.
first-order rate constant the rate constant of a first-order reaction.
first-order reaction (unimolecular reaction) a reaction whose rate is dependent on the concentration of one reactant.
Fischer esterification the reaction of a carboxylic acid with excess alcohol in the presence of an acid catalyst to form an ester.
Fischer projection a method of representing the spatial arrangement of groups bonded to a chirality centre. The chirality centre is the point of intersection of two perpendicular lines; the horizontal lines represent bonds that project out of the plane of the paper toward the viewer, and the vertical lines represent bonds that point back from the plane of the paper away from the viewer.
flagpole hydrogens (transannular hydrogens) the two hydrogens in the boat conformation of cyclohexane that are closest to each other.
Fourier transform NMR a technique in which all the nuclei are excited simultaneously by a radio frequency pulse, their relaxation monitored, and the data mathematically converted to a spectrum.
free energy of activation (ΔG#) the true energy barrier to a reaction.
free induction decay relaxation of excited nuclei.
frequency the velocity of a wave divided by its wavelength (in units of cycles/s).
Friedel–Crafts acylation an electrophilic substitution reaction that puts an acyl group on a benzene ring.
Friedel–Crafts alkylation an electrophilic substitution reaction that puts an alkyl group on a benzene ring.
frontier orbital analysis determining the outcome of a pericyclic reaction using frontier orbitals.
frontier orbitals the HOMO and the LUMO.
frontier orbital theory a theory that, like the conservation of orbital symmetry theory, explains the relationships among reactant, product and reaction conditions in a pericyclic reaction.
functional group the centre of reactivity in a molecule.
functional group inter-conversion conversion of one functional group into another functional group.
functional group region the left-hand two-thirds of an infrared spectrum where most functional groups show absorption bands.
furanose a five-member ring sugar.
furanoside a five-member ring glycoside.
fused bicyclic compound a bicyclic compound in which the rings share two adjacent carbons.
Gabriel synthesis conversion of an alkyl halide into a primary amine using phthalimide as a starting material.
gauche X and Y are gauche to each other.
gauche conformer a staggered conformer in which the largest substituents are gauche to each other.
gauche interaction the interaction between two atoms or groups that are gauche to each other.
gem-diol a compound with two OH groups on the same carbon.
geminal coupling the mutual splitting of two nonidentical protons bonded to the same carbon.
geminal dihalide a compound with two halogen atoms bonded to the same carbon.
gene a segment of DNA.
general-acid catalysis catalysis in which a proton is transferred to the reactant during the slow step of the reaction.
general-base catalysis catalysis in which a proton is removed from the reactant during the slow step of the reaction.
geometric isomers cis-trans (or E-Z) isomers.
Gibbs standard free energy change the difference between the free energy content of the products and the free energy content of the reactants at equilibrium under standard conditions (1 M, 25 °C, 1 atm).
Gilman reagent a dialkylcopper reagent used to replace a halogen with an alkyl group.
glycoside the acetal of a sugar.
glycosidic bond the bond between the anomeric carbon and the alcohol in a glycoside.
Grignard reagent the compound that results when magnesium is inserted between the carbon and halogen of an alkyl halide (RMgBr, RMgCI).
ground-state electronic configuration a description of which orbitals the electrons of an atom or molecule occupy when they are all in their lowest-energy orbitals.
half chair conformation the least stable conformation of cyclohexane.
haloform reaction the reaction of a halogen and HO with a methyl ketone.
halogenation reaction with halogen (Br2, Cl2).
halohydrin an organic molecule that contains a halogen and an OH group on adjacent carbons.
hard and soft acids and bases a classification of acids and bases depending on their polarizability. [Hard bases include fluoride ions; soft bases include triphenylphosphine. Hard acids include Na+, whilst an example of a soft, polarisable acid is Pt2+; hard-hard and soft-soft interactions are favoured. Hardness and softness can be described in terms of the HOMO and LUMO interactions].
Haworth projection a way to show the structure of a sugar; the five-and six-member rings are represented as being flat.
head-to-tail addition the head of one molecule is added to the tail of another molecule.
heat of combustion the amount of heat given off when a carbon-containing compound reacts completely with O2 to form CO2 and H2O.
heat of formation the heat given off when a compound is formed from its elements under standard conditions.
heat of hydrogenation the heat (Δ) released in a hydrogenation reaction.
Heisenberg uncertainty principle states that both the precise location and the momentum of an atomic particle cannot be simultaneously determined.
Hell-Volhard-Zelinski (HVZ) reaction heating a carboxylic acid with Br2 + P in order to convert it into an α-bromocarboxylic acid.
hemiacetal
hemiketal
Henderson–Hasselbalch equation pKa = pH + log [HA]/[A].
Heptose a monosaccharide with 7 carbons.
HETCOR spectrum A 2-D NMR spectrum that shows coupling between protons and the carbons to which they are attached.
heterocyclic compound (heterocycle) a cyclic compound in which one or more of the atoms of the ring are hetero atoms.
heterogeneous catalyst a catalyst that is insoluble in the reaction mixture.
heterolytic bond cleavage (heterolysis) breaking a bond with the result that both bonding electrons stay with one of the atoms.
hexose a monosaccharide with six carbons.
high-energy bond a bond that releases a great deal of energy when it is broken.
highest occupied molecular orbital (HOMO) the molecular orbital of highest energy that contains an electron.
high-resolution NMR spectroscopy NMR spectroscopy that uses a spectrometer with a high operating frequency.
Hofmann degradation exhaustive methylation of an amine, followed by reaction with Ag2O, followed by heating to achieve a Hofmann elimination reaction.
Hofmann elimination (anti-Zaitsev elimination) a hydrogen is removed from the β-carbon bonded to the most hydrogens.
Hofmann elimination reaction elimination of a proton and a tertiary amine from a quaternary ammonium hydroxide.
Hofmann rearrangement conversion of an amide into an amine using Br2/HO.
homogeneous catalyst a catalyst that is soluble in the reaction mixture.
homolog a member of a homologous series.
homologous series a family of compounds in which each member differs from the next by one methylene group.
homolytic bond cleavage (homolysis) breaking a bond with the result that each of the atoms gets one of the bonding electrons.
homopolymer a polymer that contains only one kind of monomer.
homotopic hydrogens two hydrogens bonded to a carbon that is bonded to two other groups that are identical.
hormone an organic compound synthesized in a gland and delivered by the bloodstream to its target tissue.
Hückel’s rule states that for a compound to be aromatic its cloud of electrons must contain (4n + 2) π electrons, where n is an integer. This is the same as saying it must contain an odd number of pairs of π electrons.
Hund’s rule states that when there are degenerate orbitals, an electron will occupy an empty orbital before it will pair up with another electron.
Hunsdiecker reaction conversion of a carboxylic acid into an alkyl halide by heating a heavy metal salt of the carboxylic acid with bromine or iodine.
hybridization the process whereby atomic orbitals of different type but similar energies are combined to form a set of equivalent hybid orbitals. These hybrid orbitals do not exist in the atoms but only in the formation of molecular orbitals by combining atomic orbitals from different atoms.
hybridized orbital an orbital formed by mixing (hybridizing) orbitals.
hydrate (gem-diol)
hydrated when water has been added to a compound.
hydration addition of water to a compound.
hydrazone R2C=NNH2
hydride ion a negatively charged hydrogen.
1,2-hydride shift the movement of a hydride ion from one carbon to an adjacent carbon.
hydroboration-oxidation the addition of borane to an alkene or an alkyne followed by reaction with hydrogen peroxide and hydroxide ion.
hydrocarbon a compound that contains only carbon and hydrogen.
α-hydrogen a hydrogen bonded to the carbon adjacent to a carbonyl carbon.
hydrogenation addition of hydrogen.
hydrogen bond an unusually strong dipole-lipole attraction (5 Kcal/mol) between a hydrogen bonded to O, N, or F and the nonbonding electrons of an O, N, or F of another molecule.
hydrogen ion (a proton) a positively charged hydrogen.
hydrolysis reaction with water.
hydrophobic interactions interactions between nonpolar groups. They increase stability by decreasing the amount of structured water (increasing entropy).
hyperconjugation delocalization of electrons by overlap of carbon–hydrogen or carbon–carbon σ bonds with an empty p orbital.
imine R2C=NR
inclusion compound a compound that specifically binds a metal ion or an organic molecule.
induced dipole–induced dipole interaction an interaction between a temporary dipole in one molecule and the dipole the temporary dipole induces in another molecule.
inductive electron donation donation of electrons through a σ bond.
inductive electron withdrawal withdrawal of electrons through a σ bond.
infrared radiation electromagnetic radiation familiar to us as heat.
infrared spectroscopy uses infrared energy to provide a knowledge of the functional groups in a compound.
infrared (IR) spectrum a plot of relative absorption versus wave number (or wavelength) of infrared radiation.
initiation step the step in which radicals are created, or the step in which the radical needed for the first propagation step is created.
intermediate a species formed during a reaction that is not the final product of the reaction.
intermolecular reaction a reaction that takes place between two molecules (same or different).
internal alkyne an alkyne with the triple bond not at the end of the carbon chain.
intimate ion pair the covalent bond that joined the cation and the anion has broken, but the cation and anion are still next to each other.
intramolecular reaction a reaction that takes place within a molecule.
inversion of configuration turning the carbon inside-out like an umbrella in a windstorm so that the resulting product has a configuration opposite to that of the reactant.
iodoform test addition of I2/HO to a methyl ketone forms a yellow precipitate.
ion–dipole interaction the interaction between an ion and the dipole of a molecule.
ion-exchange chromatography a technique that uses a column packed with an insoluble resin to separate compounds on the basis of their charges and polarities.
ionic bond a bond formed through the attraction of two ions of opposite charges.
ionization energy the energy required to remove an electron from an atom.
ionophore a compound that binds metal ions tightly.
iron protoporphyrin IX the porphyrin ring system of heme plus an iron atom.
isoelectric point (pI) the pH at which there is no net charge on an amino acid.
isolated double bonds double bonds separated by more than one single bond.
isomers nonidentical compounds with the same molecular formula.
isoprene rule head-to-tail linkage of isoprene units.
isotactic polymer a polymer in which all the substituents are on the same side of the fully extended carbon chain.
isotopes atoms with the same number of protons but different numbers of neutrons.
iterative synthesis a synthesis in which a reaction sequence is carried out more than once.
IUPAC nomenclature systematic nomenclature.
Kekule structure a model that represents the bonds between atoms as lines.
ketal
keto-enol tautomerism (keto-enol interconversion) interconversion of keto and enol tautomers.
Keto-nol tautomers a ketone and its isomeric α, β-unsaturated alcohol.
ketone
ketose a polyhydroxyketone.
Kiliani–Fischer synthesis a method used to increase the number of carbons in an aldose by one, resulting in the formation of a pair of C-2 epimers.
kinetic control when a reaction is under kinetic control, the relative amounts of the products depend on the rates at which they are formed.
kinetic isotope effect a comparison of the rate of reaction of a compound with the rate of reaction of an identical compound in which one of the atoms has been replaced by an isotope.
kinetic product the product that is formed the fastest.
kinetic resolution separation of enantiomers based on the difference in their rate of reaction with an enzyme.
kinetics the field of chemistry that deals with the rates of chemical reactions.
kinetic stability chemical reactivity, indicated by ΔG#. If ΔG# is large, the compound is kinetically stable (not very reactive). If ΔG# is small, the compound is kinetically unstable (very reactive).
Kolbe–Schmitt carboxylation reaction a reaction that uses CO2 to carboxylate phenol.
lactam a cyclic amide.
lactone a cyclic ester.
leaving group the group that is displaced in a nucleophilic substitution reaction.
Le Chatelier’s principle states that if equilibrium is disturbed, the components of the equilibrium will adjust in a way that will offset the disturbance.
levorotatory the enantiomer that rotates polarized light in a counterclockwise direction.
Lewis acid a substance that accepts an electron pair.
Lewis base a substance that donates an electron pair.
Lewis structure a model that represents the bonds between atoms as lines or dots and the valence electrons as dots.
ligation sharing of nonbonding electrons with a metal.
linear combination of atomic orbitals (LCAO) the combination of p atomic orbitals to produce a molecular orbital.
linear conjugation the atoms in the conjugated system are in a linear arrangement.
linear synthesis a synthesis that builds a molecule step by step from starting materials.
lipid a water-insoluble compound found in a living system.
living polymer a nonterminated chain-growth polymer that remains active. This means that the polymerization reaction can continue on addition of more monomer.
λmax the wavelength at which there is maximum ultraviolet/visible absorbance.
localized electrons electrons that are restricted to a particular locality.
lock-and-key model a model that describes the specificity of an enzyme for its substrate: the substrate fits the enzyme like a key fits a lock.
lone pair electrons (nonbonding electrons) valence electrons not used in bonding.
long-range coupling splitting of a proton by a proton more than three σ bonds away.
lowest unoccupied molecular orbital (LUMO) the molecular orbital of lowest energy that does not contain an electron.
Lucas test a test that determines whether an alcohol is primary, secondary, or tertiary.
magnetic anisotropy the term used to describe the greater freedom of a π electron cloud to move in response to a magnetic field as a consequence of its greater polarizability compared with σ electrons.
magnetic resonance imaging (MRI) NMR used in medicine. The difference in the way water is bound in different tissues produces the signal variation between organs as well as between healthy and diseased states.
magnetogyric ratio a property (measured in rad T−1 s−1) that depends on the magnetic properties of a particular kind of nucleus.
malonic ester synthesis synthesis of a carboxylic acid using diethyl malonate as the starting material.
Markovnikov’s rule the actual rule is: “when a hydrogen halide adds to an asymmetrical alkene, the addition occurs such that the halogen attaches itself to the sp2 carbon of the alkene bearing the lowest number of hydrogen atoms.” A more useful version is: the electrophile adds to the sp2 carbon that is bonded to the greater number of hydrogens.
mass number the number of protons plus the number of neutrons in an atom.
mass spectrometry provides a knowledge of the molecular weight, molecular formula and certain structural features of a compound.
mass spectrum a plot of the relative abundance of the positively charged fragments produced in a mass spectrometer versus their m/z values.
materials science the science of creating new materials to be used in place of known materials such as metal, glass, wood, cardboard and paper.
McLafferty rearrangement rearrangement of the molecular ion of a ketone. The bond between the α- and β-carbons breaks, and a γ-hydrogen migrates to the oxygen.
mechanism-based inhibitor (suicide inhibitor) a compound that inactivates an enzyme by undergoing part of its normal catalytic mechanism.
mechanism of a reaction a description of the step-by-step process by which reactants are changed into products.
melting point the temperature at which a solid becomes a liquid.
membrane the material that surrounds the cell in order to isolate its contents.
mercaptan (thiol) the sulphur analog of an alcohol (RSH).
meso compound a compound that contains chirality centres and a plane of symmetry.
metabolism reactions living organisms carry out in order to obtain the energy they need and to synthesize the compounds they require.
meta-directing substituent a substituent that directs an incoming substituent meta to an existing substituent.
metal-activated enzyme an enzyme that has a loosely bound metal ion.
metal-ion catalysis catalysis in which the species that facilitates the reaction is a metal ion.
metalloenzyme an enzyme that has a tightly bound metal ion.
methine hydrogen a tertiary hydrogen.
methylene group a CH2 group.
1,2-methyl shift the movement of a methyl group with its bonding electrons from one carbon to an adjacent carbon.
micelle a spherical aggregation of molecules each with a long hydrophobic tail and a polar head, arranged so that the polar head points to the outside of the sphere.
Michael reaction the addition of an α-carbanion to the β-carbon of an α,β-unsaturated carbonyl compound.
mixed anhydride an acid anhydride with two different R groups (RCO2COR’)
mixed Claisen condensation a Claisen condensation in which two different esters are used.
mixed triacylglycerol a triacylglycerol in which the fatty acid components are different.
molar absorptivity the absorbance obtained from a 1.00-M solution in a cell with a 1.00-cm light path.
molecular modeling computer-assisted design of a compound with a structure similar to that of a compound with the desired activity.
molecular modification changing the structure of a lead compound.
molecular orbital an orbital associated with a molecule.
molecular orbital theory describes a model in which the electrons occupy orbitals as they do in atoms but with the orbitals extending over the entire molecule.
molecular recognition the recognition of one molecule by another as a result of specific interactions; for example, the specificity of an enzyme for its substrate.
molozonide an unstable intermediate containing a five-member ring with three oxygens in a row that is formed from the reaction of an alkene with ozone.
monomer a repeating unit in a polymer.
monosaccharide (simple carbohydrate) a single sugar molecule.
monoterpene a terpene that contains ten carbons.
MRI scanner an NMR spectrometer used in medicine for whole body NMR.
multiplet an NMR signal split into more than seven peaks.
multiplicity the number of peaks in an NMR signal.
multistep synthesis preparation of a compound by a route that requires several steps.
mutarotation a slow change in optical rotation to an equilibrium value.
N + 1 rule an 1H NMR signal for a hydrogen with N equivalent hydrogens bonded to an adjacent carbon is split into N + 1 peaks. A 13C NMR signal for a carbon bonded to N hydrogens is split into N + 1 peaks.
N-glycoside a glycoside with a nitrogen instead of an oxygen at the glycosidic linkage.
N-terminal acid the terminal amino acid of a peptide (or protein) that has a free amino group.
natural abundance atomic weight the average mass of the atoms in the naturally occurring element.
natural product a product synthesized in nature.
neurotransmitter a compound that transmits nerve impulses.
nicotinamide adenine dinucleotide (NAD+) a coenzyme required in certain oxidation reactions. It is reduced to NADH, which can act as a reducing agent in another reaction.
nicotinamide adenine dinucleotide phosphate (NADP+) a coenzyme required in certain oxidation reactions. It is reduced to NADPH, which can act as a reducing agent in another reaction.
nitration substitution of a nitro group (NO2) for a hydrogen of a benzene ring.
nitrile a compound that contains a carbon-nitrogen triple bond (R≡CN).
nitrosamine (N-nitroso compound) R2NN=O.
NMR spectroscopy the absorption of electromagnetic radiation to determine the structural features of an organic compound. In the case of 1H NMR spectroscopy, it determines the carbon-hydrogen framework.
node that part of an orbital in which there is zero probability of finding an electron.
nominal mass mass rounded to the nearest whole number.
nonbonding molecular orbital the p orbitals are too far apart to overlap significantly, so the molecular orbital that results neither favours nor disfavours bonding.
nonpolar covalent bond a bond formed between two atoms that share the bonding electrons equally.
non-reducing sugar a sugar that cannot be oxidized by reagents such as Ag+ and Cu+. Non-reducing sugars are not in equilibrium with the open-chain aldose or ketose.
normal alkane (straight-chain alkane) an alkane in which the carbons form a continuous chain with no branches.
nucleic acid the two kinds of nucleic acid are DNA and RNA.
nucleophile an electron-rich atom or molecule.
nucleophilic acyl Substitution reaction a reaction in which a group bonded to an acyl or aryl group is substituted by another group.
nucleophilic addition–elimination reaction a nucleophilic addition reaction that is followed by an elimination reaction. Imine formation is an example: an amine adds to the carbonyl carbon and water is eliminated.
nucleophilic addition reaction a reaction that involves the addition of a nucleophile to a reagent.
nucleophilic aromatic substitution a reaction in which a nucleophile substitutes for a substituent of an aromatic ring.
nucleophilic catalyst a catalyst that increases the rate of a reaction by acting as a nucleophile.
nucleophilicity a measure of how readily an atom or molecule with a pair of non-bonding electrons attacks an atom except hydrogen.
nucleophilic substitution reaction a reaction in which a nucleophile substitutes for an atom or group.
octet rule states that an atom will give up, accept, or share electrons in order to achieve a filled shell. Because a filled second shell contains eight electrons, this is known as the octet rule.
off-resonance decoupling the mode in 13C NMR spectroscopy in which spin-spin splitting occurs between carbons and the hydrogens attached to them.
oil a triester of glycerol that exists as a liquid at room temperature.
olefin an alkene.
oligomer a protein with more than one peptide chain.
optical isomers stereoisomers that contain chirality centres. Optically active (chiral) rotates the plane of polarized light.
orbital the volume of space around the nucleus in which an electron is most likely to be found.
orbital hybridization mixing of orbitals.
organic compound a compound that contains carbon.
organic synthesis preparation of organic compounds from other organic compounds.
organometallic compound a compound containing a carbon–metal bond.
orphan drugs drugs for diseases or conditions that affect fewer than 200,000 people.
ortho/para-directing substituent a substituent that directs an incoming substituent ortho and para to an existing substituent.
osazone the product obtained by treating an aldose or a ketose with excess Phenylhydrazine. An osazone contains two imine bonds.
overtone band occurs at a multiple of the fundamental absorption frequency (2v1, 3v1).
oxidation loss of electrons by an atom or molecule.
oxidation-reduction reaction (redox reaction) a reaction that involves the transfer of electrons from one species to another.
oxidative cleavage an oxidation reaction that cuts the reactant into two or more pieces.
oxime R2C=NOH
oxirane (epoxide) an ether in which the oxygen is incorporated into a three-member ring.
oxonium ion a compound with a positively charged oxygen.
oxyanion a compound with a negatively charged oxygen.
oxymercuration addition of water using a mercuric salt of a carboxylic acid as a catalyst.
ozonide the five-member ring compound formed as a result of rearrangement of a molozonide.
ozonolysis reaction of a carbon–carbon double or triple bond with ozone.
packing the fitting of individual molecules into a frozen crystal lattice.
paraffin an alkane.
parent hydrocarbon the longest continuous carbon chain in a molecule.
parent ion (molecular ion) peak in the mass spectrum with the greatest m/z.
partial hydrolysis a technique that hydrolyzes only some of the peptide bonds in a polypeptide.
partial racemization formation of a pair of enantiomers in unequal amounts.
Pauli exclusion principle states that no more than two electrons can occupy an orbital and that the two electrons must have opposite spin.
pentose a monosaccharide with five carbons.
peptide polymer of amino acids linked together by amide bonds. A peptide contains fewer amino acid residues than a protein.
peptide bond the amide bond that links the amino acids in a peptide or protein.
pericyclic reaction a concerted reaction that takes place as the result of a cyclic rearrangement of electrons.
peroxy acid a carboxylic acid with an OOH group instead of an OH group.
perspective formula a method of representing the spatial arrangement of groups bonded to a chirality centre. Two bonds are drawn in the plane of the paper; a solid wedge is used to depict a bond that projects out of the plane of the paper toward the viewer, and a dashed line is used to represent a bond that projects back from the plane of the paper away from the viewer.
pH the pH scale is used to describe the acidity of a solution (pH = −log [H+]).
pH-activity profile a plot of the activity of an enzyme as a function of the pH of the reaction mixture.
phase transfer catalysis catalysis of a reaction by providing a way to bring a polar reagent into a nonpolar phase so that the reaction between a polar and a nonpolar compound can occur.
phase transfer catalyst a compound that carries a polar reagent into a nonpolar phase.
phenylhydrazone R2C=NNHC6H5
phosphoacylglycerol (phosphoglyceride) formed when two OH groups of glycerol form esters with fatty acids and the terminal OH group forms a phosphate ester.
phosphoanhydride bond the bond holding two phosphoric acid molecules together.
phospholipid a lipid that contains a phosphate group.
phosphoryl transfer reaction the transfer of a phosphate group from one compound to another.
photochemical reaction a reaction that takes place when a reactant absorbs light.
photosynthesis the synthesis of glucose and O2 from CO2 and H2O.
pi (π) bond a bond formed as a result of side-to-side overlap of p orbitals.
pi-complex a complex formed between an electrophile and a π bond.
pinacol rearrangement rearrangement of a vicinal diol.
pKa describes the tendency of a compound to lose a proton (pKa = − log Ka, where Ka is the acid dissociation constant).
plane of symmetry an imaginary plane that bisects a molecule into a pair of mirror images.
plasticizer an organic molecule that dissolves in a polymer and allows the polymer chains to slide by each other.
polar covalent bond a bond formed by the unequal sharing of electrons.
polarimeter an instrument that measures the rotation of polarized light.
polarizability an indication of the ease with which the electron cloud of an atom can be distorted.
polarized light light that oscillates only in one plane.
polar reaction the reaction between a nucleophile and an electrophile.
polyamide a polymer in which the monomers are amides.
polycarbonate a step-growth polymer in which the dicarboxylic acid is carbonic acid.
polyene a compound that has several double bonds.
polyester a polymer in which the monomers are esters.
polymer a large molecule made by linking monomers together.
polymer chemistry the field of chemistry that deals with synthetic polymers; part of the larger discipline known as materials science.
polymerization the process of linking up monomers to form a polymer.
polypeptide many amino acids linked by amide bonds.
polysaccharide a compound containing ten or more sugar molecules linked together.
polyunsaturated fatty acid a fatty acid with more than one double bond.
polyurethane a polymer in which the monomers are urethanes.
primary alcohol an alcohol in which the OH group is bonded to a primary carbon.
primary alkyl halide an alkyl halide in which the halogen is bonded to a primary carbon.
primary amine an amine with one alkyl group bonded to the nitrogen.
primary carbocation a carbocation with the positive charge on a primary carbon.
primary carbon a carbon bonded to only one other carbon.
primary hydrogen a hydrogen bonded to a primary carbon.
primary radical a radical with the unpaired electron on a primary carbon.
prochirality centre a carbon bonded to two hydrogens that will become a chirality centre if one of the hydrogens is replaced by deuterium.
propagating site the reactive end of a chain-growth polymer.
propagation step in the first of a pair of propagation steps, a radical (or an electrophile or a nucleophile) reacts to produce another radical (or am electrophile or a nucleophile) that reacts in the second propagation step to produce the radical (or the electrophile or the nucleophile) that was the reactant in the first propagation step.
pro-R-hydrogen replacing this hydrogen with deuterium creates a chirality centre with the R configuration.
pro-S-hydrogen replacing this hydrogen with deuterium creates a chirality centre with the S configuration.
pro-chiral carbonyl carbon a carbonyl carbon that will become a chirality centre if it is attacked by a group unlike any of the groups already bonded to it.
protecting group a reagent that protects a functional group from a synthetic operation that it would otherwise not survive.
protic solvent a solvent that has a hydrogen bonded to an oxygen or a nitrogen.
proton a positively charged hydrogen; a positively charged particle in an atomic nucleus.
proton-decoupled 13C NMR spectrum a 13C NMR spectrum in which all the signals appear as singlets because there is no coupling between the 13C nucleus and its bonded hydrogens.
proton transfer reaction a reaction in which a proton is transferred from an acid to a base.
protoporphyrin IX the porphyrin ring system of heme.
pseudo first-order reaction a second-order reaction in which the concentration of one of the reactants is much greater than the other, which allows the reaction to be treated as a first-order reaction.
pyranose a six-member ring sugar.
pyranoside a six-member ring glycoside.
pyridoxal-phosphate the coenzyme required by enzymes that catalyze certain transformations of amino acids.
quantum numbers numbers arising from the quantum mechanical treatment of an atom that describe the properties of the electrons in the atom.
quartet an NMR signal split into four peaks.
quaternary ammonium ion an ion containing a nitrogen bonded to four alkyl groups (R4N+).
quaternary ammonium salt a quaternary ammonium ion and an anion (R4N+X).
quaternary structure a description of the way the individual polypeptide chains of a protein are arranged with respect to each other.
racemic mixture (racemate, racemic modification) a mixture of equal amounts of a pair of enantiomers.
radical an atom or molecule with an unpaired electron.
radical addition reaction an addition reaction in which the first species that adds is a radical.
radical anion a species with a negative charge and an unpaired electron.
radical cation a species with a positive charge and an unpaired electron.
radical chain reaction a reaction in which radicals are formed and react in repeating propagating steps.
radical inhibitor a compound that traps radicals.
radical initiator a compound that creates radicals.
radical reaction a reaction in which a new bond is formed using one electron from one reagent and one electron from another reagent.
radical substitution reaction a substitution reaction that has a radical intermediate.
rate constant a measure of how easy it is to reach the transition state of a reaction (to get over the energy barrier to the reaction).
rate-determining step (rate-limiting step) the step in a reaction that has the transition state with the highest energy.
rational drug design designing drugs with a particular structure to achieve a specific purpose.
R configuration after assigning relative priorities to the four groups bonded to a chirality centre, if the lowest-priority group is on a vertical axis in a Fischer projection (or pointing away from the viewer in a perspective formula), an arrow drawn from the highest priority group to the next-highest-priority group goes in a clockwise direction.
red shift a shift to a longer wavelength.
reducing sugar a sugar that can be oxidized by reagents such as Ag+ and Cu+. Reducing sugars are in equilibrium with the open-chain aldose or ketose.
reduction gain of electrons by an atom or molecule.
reductive amination the reaction of an aldehyde or a ketone with ammonia or with a primary amine in the presence of a reducing agent (H2/Raney Ni).
reference compound a compound added to the sample whose NMR spectrum is to be taken. The positions of the signals in the NMR spectrum are measured from the position of the signal given by the reference compound.
regioselective reaction a reaction that leads to the preferential formation of one constitutional isomer over another.
relative configuration the configuration of a compound relative to the configuration of another compound.
resolution of a racemic mixture separation of a racemic mixture into the individual enantiomers.
resonance a compound with delocalized electrons is said to have resonance.
resonance contributor (resonance structure) a structure with localized electrons that approximates the true structure of a compound with delocalized electrons.
resonance electron donation donation of electrons through p orbital overlap with neighbouring π bonds.
resonance electron withdrawal withdrawal of electrons through p orbital overlap with neighbouring π bonds.
resonance hybrid the actual structure of a compound with delocalized electrons; it is represented by two or more structures with localized electrons.
resonances NMR absorption signals.
retrosynthesis (retrosynthetic analysis) working backward (on paper) from the target molecule to available starting materials.
rf-flip radiation radiation in the radiofrequency region of the electromagnetic spectrum.
ribonucleic acid (RNA) a polymer of ribonucleotides.
ribonucleotide a nucleotide in which the sugar component is D-ribose.
ring current the movement of π electrons around a benzene ring.
ring-expansion rearrangement rearrangement of a carbocation in which the positively charged carbon is bonded to a cyclic compound and as a result of rearrangement the size of the ring increases by one carbon.
ring-flip (chair-chair intereonversion) the conversion of the chair conformer of cyclohexane into the other chair conformer. Bonds that are axial in one chair conformer are equatorial in the other chair conformer.
ring-opening polymerization a chain-growth polymerization that involves opening the ring of the monomer.
Ritter reaction reaction of a nitrile with a secondary or tertiary alcohol to form a secondary amide.
Robinson annulation a Michael reaction followed by an intramolecular aldol condensation.
Rosenmund reduction reduction of an acyl chloride to an aldehyde using H2 and a deactivated palladium catalyst.
Ruff degradation a method used to shorten an aldose by one carbon.
Sandmeyer reaction the reaction of an aryl diazonium salt with a cuprous salt.
saponification hydrolysis of a fat under basic conditions.
saturated hydrocarbon a hydrocarbon that is completely saturated with hydrogen (contains no double or triple bonds).
sawhorse projection the sideways projection of a carbon–carbon single bond and the attached substituents. [It gives a clearer representation of stereochemistry than the Fischer projection. See also Newmann projection].
Schiemann reaction the reaction of an aryl diazonium salt with HBF4.
Schiff base R2C=NR
s-cis-conformation the conformation in which two double bonds are on the same side of a single bond.
S configuration after assigning relative priorities to the four groups bonded to a chirality centre, if the lowest-priority group is on a vertical axis in a Fischer projection (or pointing away from the viewer in a perspective formula), an arrow drawn from the highest-priority group to the next-highest-priority group goes in a counterclockwise direction.
secondary alcohol an alcohol in which the OH group is bonded to a secondary carbon.
secondary alkyl halide an alkyl halide in which the halogen is bonded to a secondary carbon.
secondary amine an amine with two alkyl groups bonded to the nitrogen.
secondary carbocation a carbocation with the positive charge on a secondary carbon.
secondary carbon a carbon bonded to two other carbons.
secondary hydrogen a hydrogen bonded to a secondary carbon.
secondary radical a radical with the unpaired electron on a secondary carbon.
secondary structure a description of the conformation of the backbone of a protein.
second-order rate constant the rate constant of a second-order reaction.
selection rules the rules that determine the outcome of a pericyclic reaction.
selenenylation reaction conversion of an α-bromoketone into an α, β-unsaturated ketone via formation of an α-phenylseleno ketone.
semicarbazone R2C=NNHCONH2
separated charges a positive and a negative charge that can be neutralized by the movement of electrons.
sesquiterpene a terpene that contains 15 carbons.
shielding caused by electron donation to the environment of a proton. The electrons shield the proton from the full effect of the applied magnetic field. The more a proton is shielded, the farther to the right its signal appears in an NMR spectrum.
sigma (σ) bond a bond with a symmetrical distribution of electrons.
sigmatropic rearrangement a reaction in which a σ bond is broken in the reactant, a new σ bond is formed in the product, and the π bonds rearrange.
Simmons–Smith reaction formation of a cyclopropane using CH2I2 + Zn(Cu).
simple triacylglycerol a triacylglycerol in which the fatty acid components are the same.
single bond a σ bond.
singlet an unsplit NMR signal.
SN1 reaction a first-order nucleophilic substitution reaction.
SN2 reaction a second-order nucleophilic substitution reaction.
SNAr reaction a nucleophilic aromatic substitution reaction.
soap a sodium or potassium salt of a fatty acid.
solid-phase synthesis a technique in which one end of the compound being synthesized is covalently attached to a solid support.
solvation the interaction between a solvent and another molecule (or ion).
solvent-separated ion pair the cation and anion are separated by a solvent molecule.
solvolysis reaction with the solvent.
specific-acid catalysis catalysis in which the proton is fully transferred to the reactant before the slow step of the reaction
specific-base catalysis catalysis in which the proton is completely removed from the reactant before the slow step of the reaction.
specific rotation the amount of rotation that will be caused by a compound with a concentration of 1.0 g/mL in a sample tube 1.0 dm long.
spectroscopy study of the interaction of matter and electromagnetic radiation.
spin-coupled 13C NMR spectrum a 13C NMR spectrum in which each signal for a carbon is split by the hydrogens bonded to that carbon.
spin-coupling the atom that gives rise to an NMR signal is coupled to the rest of the molecule.
spin-decoupling the atom that gives rise to an NMR signal is decoupled from the rest of the molecule.
spin-spin coupling the splitting of a signal in an NMR spectrum described by the N + 1 rule.
α-spin state nuclei in this spin state have their magnetic moments oriented in the same direction as the applied magnetic field.
β-spin state nuclei in this spin state have their magnetic moments oriented opposite to the direction of the applied magnetic field.
spirocyclic compound a bicyclic compound in which the rings share one carbon.
staggered conformation a conformation in which the bonds on one carbon bisect the bond angle on the adjacent carbon when viewed looking down the carbon–carbon bond.
stereochemistry the field of chemistry that deals with the structures of molecules in three dimensions.
stereoelectronic effects the combination of steric effects and electronic effects.
stereoisomers isomers that differ in the way the atoms are arranged in space.
stereoselective reaction a reaction that leads to the preferential formation of one stereoisomer over another.
stereospecific reaction a reaction in which the reactant can exist as stereoisomers and each stereoisomeric reactant leads to a different stereoisomeric product.
steric effects effects due to the fact that groups occupy a certain volume of space.
steric hindrance refers to bulky groups at the site of a reaction that make it difficult for the reactants to approach each other.
steric strain (van der Waals strain or van der Waals repulsion) the repulsion between the electron cloud of an atom or group of atoms and the electron cloud of another atom or group of atoms.
steroid a class of compounds that contains a steroid ring system.
Stork enamine reaction that uses an enamine as a nucleophile in a Michael reaction.
s-trans-conformation a conformation in which two double bonds are on opposite sides of a single bond.
Strecker synthesis a method used to synthesize an amino acid: an aldehyde reacts with NH3, forming an imine that is attacked by cyanide ion. Hydrolysis of the product gives am amino acid.
stretching frequency the frequency at which a stretching vibration occurs.
stretching vibration a vibration occurring along the line of the bond.
structural protein a protein that gives strength to a biological structure.
α-substituent a substituent on the opposite side of a steroid ring system as the angular methyl groups.
β-substituent a substituent on the same side of a steroid ring system as the angular methyl groups.
α-substitution reaction a reaction that puts a substituent on an α-carbon in place of am α-hydrogen.
substrate the reactant of an enzyme-catalyzed reaction.
subunit am individual chain of an oligomer.
sulphide (thioether) the sulphur analog of an ether (RSR).
sulphonate ester the ester of a sulphonic acid (RSO2OR).
sulphonation substitution of a hydrogen of a benzene ring by a sulphuric acid group (−SO3H).
suprafacial bond formation formation of two σ bonds from the same side of the π system.
suprafacial rearrangement rearrangement in which the migrating group remains on the same face of the π system.
symmetrical anhydride an acid anhydride with identical R groups.
symmetrical ether an ether with two identical substituents bonded to the oxygen.
symmetric molecular orbital a molecular orbital in which the left half is a mirror image of the right half.
symmetry-allowed pathway a pathway that leads to overlap of inphase orbitals.
symmetry-forbidden pathway a pathway that leads to overlap of out-of-phase orbitals.
syn addition an addition reaction in which the two added substituents add to the same side of the molecule.
syn elimination an elimination reaction in which the two substituents eliminated are removed from the same side of the molecule.
syn-periplanar parallel substituents on the same side of a molecule.
synthetic equivalent the reagent actually used as the source of a synthon.
synthetic polymer a polymer that is not synthesized in nature.
synthetic tree an outline of the available routes to get to the desired product from available starting materials.
synthon a fragment of a disconnection.
target molecule the desired end product of a synthesis.
tautomerism interconversion of tautomers.
tautomers isomers that differ in the location of a double bond and a hydrogen.
terminal alkyne an alkyne with the triple bond at the end of the carbon chain.
termination step two radicals combine to produce a molecule in which all the electrons are paired.
terpene a lipid, isolated from a plant that contains carbon atoms in multiples of 5.
terpenoid a terpene that contains oxygen.
tertiary alcohol an alcohol in which the OH group is bonded to a tertiary carbon.
tertiary alkyl halide an alkyl halide in which the halogen is bonded to a tertiary carbon.
tertiary amine an amine with three alkyl groups are bonded to the nitrogen.
tertiary carbocation a carbocation with the positive charge on a tertiary carbon.
tertiary carbon a carbon bonded to three other carbons.
tertiary hydrogen a hydrogen bonded to a tertiary carbon.
tertiary radical a radical with the unpaired electron on a tertiary carbon.
tertiary structure a description of the three-dimensional arrangement of all the atoms in a protein.
tetrahedral bond angle the bond angle (109.5°) formed by adjacent bonds of an sp3 hybridized carbon.
tetrahedral carbon an sp3 hybridized carbon; a carbon that forms covalent bonds using four sp3 hybridized orbitals.
tetrahedral intermediate the intermediate formed in a nucleophilic acyl substitution reaction.
tetraterpene a terpene that contains 40 carbons.
tetrose a monosaccharide with four carbons.
thermodynamic control when a reaction is under thermodynamic control, the relative amounts of the products depend on their stabilities.
thermodynamic product the most stable product.
thermodynamics the field of chemistry that describes the properties of a system at equilibrium.
thermodynamic stability is indicated by ΔG°. If ΔG° is negative, the products are more stable than the reactants. If ΔG° is positive, the reactants are more stable than the products.
thermoplastic polymer a polymer that has both ordered crystalline regions and amorphous noncrystalline regions.
thermosetting polymer cross-linked polymers that, after they are hardened, cannot be remelted by heating.
thiirane a three-member ring compound in which one of the ring atoms is a sulphur.
thin-layer chromatography a technique that separates compounds on the basis of their polarity.
thioester the sulphur analog of an ester. R(CO)SR.
thioether (sulphide) the sulphur analog of an ether (RSR).
thiol (mercaptan) the sulphur analog of an alcohol (RSH).
tosylation a reaction which introduces the toluene-4-sulphonyl group into a molecule. [Generally by reaction of an alcohol with tosyl chloride to give the tosylate ester].
threo enantiomers the pair of enantiomers with similar groups on opposite sides when drawn in a Fischer projection.
Tollens test an aldehyde can be identified by observation of the formation of a silver mirror in the presence of Tollens’ reagent (Ag2O/NH3).
torsional strain the repulsion felt by the bonding electrons of one substituent as they pass close to the bonding electrons of another substituent.
trademark a registered name, symbol, or picture.
transamination a reaction in which an amino group is transferred from one compound to another.
transcription the synthesis of mRNA from a DNA blueprint.
transesterification reaction the reaction of an ester with an alcohol to form a different ester.
trans fused two cyclohexane rings fused together such that if the second ring were considered to be two substituents of the first ring, both substituents would be in equatorial positions.
transimination the reaction of a primary amine with an imine to form a new imine and a primary amine derived from the original imine.
trans isomer the isomer with identical substituents on opposite sides of the double bond.
transition state the highest point on a hill in a reaction coordinate diagram. In the transition states, bonds in the reactant that will break are partially broken and bonds in the product that will form are partially formed.
transition state analog a compound that is structurally similar to the transition state of an enzyme-catalyzed reaction.
translation the synthesis of a protein from an mRNA blueprint.
transmetallation metal exchange.
triacylglycerol the compound formed when the three OH groups of glycerol are esterified with fatty acids.
triene a hydrocarbon with three double bonds.
trigonal planar carbon an sp2 hybridized carbon.
triose a monosaccharide with three carbons.
tripeptide three amino acids linked by amide bonds.
triple bond a σ bond plus two π bonds.
triplet an NMR signal split into three peaks.
triterpene a terpene that contains 30 carbons.
twist-boat (skew-boat) conformation a conformation of cyclohexane.
ultraviolet light electromagnetic radiation with wavelengths ranging from 180 to 400 nm.
ultraviolet/visible spectroscopy the absorption of electromagnetic radiation to determine information about conjugated systems.
umpolung reversing the normal polarity of a functional group.
unsaturated hydrocarbon a hydrocarbon that contains one or more double or triple bonds.
valence electron an electron in an unfilled shell.
valence shell electron pair repulsion (VSEPR) model combines the concept of atomic orbitals with the concept of shared electron pairs and the minimization of electron pair repulsion.
van der Waals forces (London forces) induced dipole–induced dipole interactions.
van der Waals radius a measure of the effective size of an atom or group. A repulsive force occurs (van der Waals repulsion) if two atoms approach each other at a distance less than the sum of their van der Waals radii.
vector sum takes into account both the magnitudes and the directions of the bond dipoles.
vicinal dihalide a compound with halogens bonded to adjacent carbons.
vicinal diol (vicinal glycol) a compound with OH groups bonded to adjacent carbons.
vinyl group CH2=CH
vinylic carbon a carbon in a carbon–carbon double bond.
vinylic cation a compound with a positive charge on a vinylic carbon.
vinylic radical a compound with an unpaired electron on a vinylic carbon.
visible light electromagnetic radiation with wavelengths ranging from 400 to 780 nm.
vitamin a substance needed in small amounts for normal body function that the body cannot synthesize or cannot synthesize in adequate amounts.
vulcanization increasing the flexibility of rubber by heating it with sulphur.
Walden inversion a Walden inversion occurs at a tetrahedral carbon atom during an SN2 reaction when the entry of the reagent and the departure of the leaving group are synchronous. The result is an inversion of configuration at the centre under attack.
wavelength distance from any point on one wave to the corresponding point on the next wave (in units of mm).
wavenumber the number of waves in 1 cm.
wax an ester formed from a long-chain carboxylic acid and a long chain alcohol.
wedge-and-dash structure a method of representing the spatial arrangement of groups bonded to a chirality centre. Wedges are used to represent bonds that point out of the plane of the paper toward the viewer, and dashed lines are used to represent bonds that point back from the plane of the paper away from the viewer.
Williamson ether synthesis formation of an ether from the reaction of an alkoxide ion with an alkyl halide.
Wittig reaction the reaction of an aldehyde or a ketone with a phosphonium ylide, resulting in formation of an alkene.
Wolff–Kishner reduction a reaction that reduces the carbonyl group of a ketone to a methylene group using NH2NH2/HO.
Woodward–Fieser rules allow the calculation of the λmax of the π → π* transition for compounds with four or fewer conjugated double bonds.
Woodward–Hoffmann rules a series of selection rules for pericyclic reactions.
ylide a compound with opposite charges on adjacent, covalently bonded atoms with complete octets.
Zaitsev’s rule the more stable alkene product is obtained by removing a proton from the β-carbon that is bonded to the fewest hydrogens.
Z conformation the conformation of a carboxylic acid or carboxylic acid derivative in which the carbonyl oxygen and the substituent bonded to the carboxyl oxygen or nitrogen are on the same side of the single bond.
Ziegler–Natta catalyst an aluminum–titanium initiator that controls the stereochemistry of a polymer.
Z isomer the isomer with the high-priority groups on the same side of the double bond.
zwitterion a compound with a negative charge and a positive charge on non-adjacent atoms.