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General Glossary

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[Please note: The entries in this table are, except where noted (*), taken directly from the glossary of Organic Chemistry , 4/E, by John McMurry. We are grateful to the publishers (Brooks/Cole) for giving their permission to use the glossary entries from that textbook in connection with our Web page project.]

Absolute configuration
The actual three-dimensional structure of a chiral molecule. Absolute configurations are specified verbally by the Cahn-Ingold-Prelog R,S convention and are represented on paper by Fischer projections.
Having a lack of handedness. A molecule is achiral if it has a plane of symmetry and is thus superimposable on its mirror image. (See "Chiral.")
Activating group
An electron-donating group such as hydroxyl (-OH) or an amino (-NH2) that increases the reactivity of an aromatic ring toward electrophilic aromatic substitution. All activating groups are ortho- and para- directing.
Activation energy
The difference in energy between the ground state and transition state. The amount of activation energy required by a reaction determines the rate at which the reaction proceeds. Most reactions have activation energies of 40-100 kJ/mol.
Acylium ion
A resonance-stabilized carbocation in which the positive charge is located at an sp-hybridized carbonyl-group carbon. Acylium ions are strongly electrophilic and are involved as intermediates in Friedel-Crafts acylation reactions.
1,4 Addition
Addition of a reagent to the ends of a conjugated pi system. Conjugated dienes yield 1,4 adducts when treated with electrophiles such as HCl. Conjugated enones yield 1,4 adducts when treated with nucleophiles such as cyanide ion.
Addition reactions
The reaction that occurs when two reactants add together to form a single new product with no atoms "left over."
Allyl group
A "-CH2CH=CH2" substituent.
Used to refer to the position next to a double bond. For example, H2C=CHCH2Br is an allylic bromide, and an allylic radical is a conjugated, resonance-stabilized species in which the unpaired electron is in a "p" orbital next to a double bond.
Alpha position
The position next to a carbonyl group.
Anti conformation
The geometric arrangement around a carbon-carbon single bond, in which the two largest substituents are 180 degrees apart as viewed in a Newman projection.
Anti stereochemistry
Referring to opposite sides of a double bond or molecule. An anti addition reaction is one in which the two ends of the double bond are attacked from different sides. For example, addition of diatomic bromine to cyclohexene yields trans-1,2-dibromocyclohexane, the product of anti addition. An anti elimination reaction is one in which the two groups leave from opposite sides of the molecule. (See "Syn stereochemistry.")
The special characteristics of cyclic conjugated pi electron systems that result from their electronic structures. These characteristics include unusual stability, the presence of a ring current in the proton NMR spectrum, and a tendency to undergo substitution reactions rather than addition reactions on treatment with electrophiles. Aromatic molecules are planar, cyclic, conjugated species that have 4n + 2 pi electrons.
Axial bond
A bond to chair cyclohexane that lies along the ring axis perpendicular to the rough plane of the ring.
Referring to the position next to an aromatic ring. For example, a benzylic carbocation is a resonance-stabilized, conjugated carbocation having its positive charge located on a carbon atom next to the benzene ring in a pi orbital that overlaps the aromatic pi system
Bimolecular reaction
A reaction whose rate-determining step occurs between two molecules.
A carbon cation, or molecule that contains a trivalent, positively charged carbon having six electrons in its outer shell. Carbocations are planar and sp2 hybridized.
Chair cyclohexane
The three-dimensional conformation of cyclohexane that resembles the rough shape of a chair. The chair form of cyclohexane, which has neither angle strain nor eclipsing strain, represents the lowest-energy conformation of the molecule.
Having handedness. Chiral molecules are those that do not have a plane of symmetry and are therefore not superimposable on their mirror image. A chiral molecule thus exists in two forms, one right-handed and one left-handed. The most common (though not the only) cause of chirality in a molecule is the presence of a carbon atom that is bonded to four different substituents. (See "Achiral.")
Chiral center
An atom (usually carbon) that is bonded to four different groups and is therefore chiral. (See "Chiral.")
Cis-trans isomers
Certain kinds of stereoisomers that differ in their stereochemistry about a double bond or on a ring. Cis-trans isomers are also called geometric isomers.
Referring to a reaction that takes place in a single step without intermediates. The SN2 displacement reaction, for example, is a concerted process.
Condensed structure
A shorthand way of writing structures in which carbon-hydrogen and carbon-carbon bonds are understood rather than shown explicitly. Propane, for example, has the condensed structure CH3CH2CH3.
The three-dimensional arrangement of atoms bonded to a chiral center relative to other chiral centers in the same molecule.
The exact three-dimensional shape of a molecule at any given instant, assuming that rotation around single bonds is frozen.
A series of alternating single and multiple bonds with overlapping p orbitals. For example, 1,3-butadiene is a conjugated diene, and the allyl cation is a conjugated carbocation.
Constitutional isomers
Isomers that have their atoms connected in a different order. For example, butane and isobutane (2-methylpropane) are constitutional isomers.
d,l form
A shorthand way of indicating the racemic modification of a compound.
Deactivating group
An electron-withdrawing substituent that decreases the reactivity of an aromatic ring toward electrophilic aromatic substitution. Most deactivating groups, such as nitro, cyano, and carbonyl, are meta-directors, but halogen substituents are ortho- and para-directors.
A reaction that involves loss of water from the starting material. Most alcohols, for example, can be dehydrated to give alkenes.
A reaction that involves loss of HX from the starting material. Alkyl halides undergo dehydrohalogenation to yield alkenes on treatment with strong base.
A spreading out of electron density over a conjugated pi electron system. For example, allylic cations and allylic anions are delocalized because their charges are spread out by resonance over the entire pi electron system.
A word used to describe an optically-active substance that rotates the plane of polarization of plane-polarized light in a right-handed (clockwise) directon. The direction of rotation is not related to the absolute configuraton of the molecule. (See "Levorotatory.")
A term that indicates the relationship between non-mirror-image stereoisomers. Diastereomers are stereoisomers that have the same configuration at one or more chiral centers, but differ at other chiral centers.
d,l form
A shorthand way of indicating the racemic modification of a compound. (See "Racemic mixture.")
Eclipsed conformation
The geometric arrangement around carbon-carbon single bonds in which the bonds to substituents on one carbon are parallel to the bonds of substituents on neighboring carbon atoms as viewed in a Newman projection.
A species that accepts an electron pair from a nucleophile in a polar bond-forming reaction.
Stereoisomers of a chiral substance that have a mirror-image relationship. Enantiomers must have opposite configurations at every chiral center in the molecule.
Entgegen (E)
A term used to describe the stereochemistry of a carbon-carbon double bond. The two groups on each carbon atom are first assigned priorities according to the Cahn-Ingold-Prelog sequence rules, and the two carbons are then compared. If the high-priority groups on each carbon are on opposite sides of the double bond, the bond has E geometry. (See Zusammen .)
Equatorial bond
A bond to cyclohexane that lies along the rough equator of the ring.
Fischer projection
A means of depicting the absolute configuration of chiral molecules on a flat page. A Fischer projection uses a cross to represent the stereogenic center. The horizontal arms of the cross represent bonds coming out of the plane of the page, and the vertical arms represent bonds going back into the plane of the page.
Gauche conformation
The conformation of butane in which the two methyl groups lie 60 degrees apart as viewed in a Newman projection. This conformation has 3.8 kJ/mol steric strain.
Geometric isomers
An old term for cis-trans isomers.
Haworth projection
A means for viewing stereochemistry in cyclic hemiacetal forms of sugars. Haworth projections are drawn so that the ring is flat and is viewed from an oblique angle with the hemiacetal oxygen at the upper right.
Addition of water to a molecule, such as occurs when alkenes are treated with aqueous sulfuric acid to give alcohols.
A weak interaction that results from overlap of a vacant p orbital on one atom with a neighboring sigma bond. Hyperconjugation is important in stabilizing carbocations and in stabilizing substituted alkenes.
A species that is formed during the course of a multistep reaction but is not the final product. Intermediates are more stable than transition states, but may or may not be stable enough to isolate.
Ionic bond
A bond between two ions due to the electrical attraction of unlike charges. Ionic bonds are formed between strongly electronegative elements (such as the halogens) and strongly electropositive elements (such as the alkali metals).
Compounds that have the same molecular formula but have different structures.
Kinetic control
Reactions that follow the lowest activation energy pathway are said to be kinetically controlled. The product formed in a kinetically controlled reaction is the one that is formed most rapidly, but is not necessarily the most stable.
Referring to reaction rates. Kinetic measurements can be extremely important in helping to determine reaction mechanisms.
Leaving group
The group that is replaced in a substitution reaction. The best leaving groups in nucleophilic substitution reactions are those that form the most stable, least basic, anions.
Used to describe an optically active substance that rotates the plane polarization of plane-polarized light in a left-handed (counterclockwise) direction.
Lone-pair electrons
Nonbonding electron pairs that occupy valence orbitals. It is the lone-pair electrons that are used by nucleophiles in their reactions with electrophiles.
Markovnikov's rule
A guide for determining the regiochemistry (orientation) of electrophilic addition reactions. In the addition of HX to an alkene, the hydrogen atom bonds to the alkene carbon that has fewer alkyl substituents. A modern statement of this rule is that electrophilic addition reactions proceed via the most stable carbocation intermediate.
A complete description of how a reaction occurs. A mechanism must account for all starting materials and all products, and must describe the details of each individual step in the overall reaction process.
Meso compound
A compound that contains stereogenic centers but is nevertheless achiral by virtue of a symmetry plane. For example, (2R,3S)-butanediol has two stereogenic carbon atoms but is achiral because of a symmetry plane between carbons 2 and 3.
Newman projection
A means of indicating stereochemical relationships between substituent groups on neighboring carbons. The carbon-carbon bond is viewed end-on, and the carbons are indicated by a circle. Bonds radiating from the center of the circle are attached to the front carbon, and bonds radiating from the edge of the circle are attached to the rear carbon.
Normal alkane
A straight-chain alkane, as opposed to a branched alkane. Normal alkanes are denoted by the prefix n, as in n -C4H10 (n -butane).
A "nucleus-lover," or species that donates an electron pair to an electrophile in a polar bond-forming reaction. Nucleophiles are also Lewis bases.
Optical isomers
An alternative name for enantiomers. Optical isomers are isomers that have a mirror-image relationship.
Optically active
A substance that rotates the plane of polarization of plane-polarized light. Note that an optically active sample must contain chiral molecules, but that all samples with chiral molecules are not optically active. Thus, a racemic sample is optically inactive even though the individual molecules are chiral.
A conformation in which bonds to neighboring atoms have a parallel arrangement. In an eclipsed conformation, the neighboring bonds are syn periplanar; in a staggered conformation, some bonds are anti periplanar, and others are "gauche."
Plane-polarized light
Ordinary light that has its electric field vectors in a single plane rather than in random planes. The plane of polarization is rotated when the light is passed through a solution of a chiral substance.
Polar aprotic solvent
A polar sovent that can't function as a hydrogen ion donor. Polar aprotic solvents such as dimethyl sulfoxide (DMSO), hexamethylphosphoramide (HMPA), and dimethylformamide (DMF) are particularly useful in SN2 reactions because of their ability to solvate cations.
The unsymmetrical distribution of electrons in a molecule that results when one atom attracts electrons more strongly than another.
The measure of the change in a molecule's electron distribution in response to changing electric interactions with solvents or ionic reagents.
Primary, Secondary, Tertiary, Quaternary
Terms used to describe the substitution pattern at a specific site. A primary site has one organic substituent attached to it, a secondary site has two organic substituents, a tertiary site has three, and a quaternary site has four.
Carbon Hydrogen Alcohol Amine
Secondary R2CH2 R2CH2 R2CHOH R2NH
Tertiary R3CH R3CH R3COH R3N
Quaternary R4C
Protic Solvent
A solvent such as water or alcohol that can act as a proton donor. Protic solvents are particularly good at stabilizing anions by hydrogen bonding, thereby lowering their reactivity.
R,S convention
A method for defining the absolute configuration at stereogenic centers using the Cahn-Ingold-Prelog sequencing rules.
Racemic Mixture
A mixture consisting of equal parts (+) and (-) enantiomers of a chiral substance. Even though the individual molecules are chiral, racemic mixtures are optically inactive.
A species that has an odd number of electrons, such as the chlorine radical, Cl-.
Rate-limiting Step
The slowest step in a multistep reaction sequence. The rate-limiting step acts as a kind of bottleneck in multistep reactions and is abserved by kinetics measurements.
Reaction energy diagram
A pictorial representation of the course of a reaction, in which potential energy is plotted as a function of reaction progress. Starting materials, transition states, intermediates, and final products are represented, and their appropriate energy levels are indicated.
A term describing the orientation of a reaction that occurs on an unsymmetrical substrate. Markovnikov's rule, for example, predicts the regiochemistry of electrophilic addition reactions.
A term describing a reaction that occurs with a specific regiochemistry to give a single product rather than a mixture of products.
Resonance effects
The effect by which substituents donate or withdraw electrons through orbital overlap with neighboring pi bonds. For example, an oxygen or nitrogen substituent donates electrons to an aromatice ring by overlap of the O or N orbital with the aromatic ring p orbitals. A carbonyl substituent, however, withdraws electron density from an aromatic ring by p orbital overlap.
Resonance hybrid
A molecule, such as benzene, that can't be represented adequately by a single Kekule structure but must instead be considered as an average of two or more resonance structures. The resonance structures themselves differ only in the positions of their electrons, not their nuclei.
The molecular motion that converts one chair conformation of cyclohexane into another chair conformation. The effect of a ring-flip is to convert an axial substituent into en equatorial substituent.
A molecule that has only single bonds and thus can't undergo addition reactions. Alkanes are saturated, but alkenes are unsatured.
Second-order reaction
A reaction whose rate-limiting step is bimolecular and whose kinetics are therefore dependent on the concentration of two reagents.
Sequence rules
A series of rules for assigning relative priorities to substituent groups on a double-bond carbon atom or on a atereogenic center. Once priorities have been established, E,Z double-bond geometry and R,S configurational assignments can be made.
Sigma bond
A covalent bond formed by head-on overlap of atomic orbitals.
sp orbital
A hybrid orbital derived forn the combination of an s and a p atomic orbital. The two sp orbitals that result from hybridization are oriented at and angle of 180 to each other.
sp2 orbital
A hybrid derived form the combination of an s atomic orbital with two p atomic orbitals. The three sp2 hybrid orbitals that result lie in a plane at angles of 120 to each other.
sp3 orbital
A hybrid orbital derived by combination of an s atomic orbital with three p atomic orbitals. The four sp3 orbitals that result are directed towards the corners of a regular tetrahedron at angles of 109 to each other.
Specific rotation, [a]D
The specific rotation of a chiral compound is a physical constant that is defined by the equation ... where the path length of the sample solution is expressed in decimeters and the concentration of the sample solution is expressed in grams per milliliter.
The branch of chemistry concerned with the three-dimensional arrangement of atoms in molecules.
Stereogenic centers
An atom (usually carbon) that is bonded to four different groups.
Isomers that have their atoms connected in the same order but have different three-dimensional arrangements. The terms stereoisomer includes both enantiomers and diastereomers but does not include constitutional isomers.
A term indicating that only a single stereoisomer is produced in a given reaction rather than a mixture.
Steric strain
The strain imposed on a molecule when two groups are too close together and try to occupy the same space. Steric strain is responsible for the greater stability of trans versus cis alkenes and for the greater stability of equatorially substituted versus axially substituted cyclohexanes.
Substitution reaction
What occurs when two reactants exchange parts to give two new products, SN1 and SN2 reactions are examples.
Symmetry plane
A plane that bisects a molecule such that one half of the molecule is the mirror image of the other half. Molecules containing a plane of symmetry are achiral.
Syn stereochemistry
A syn addition reaction is one in which the two ends of the double bond are attacked for the same side. For example OsO4 induced hydroxylation of cyclohexane yields cis-1,2-cyclohexanediol, the product of syn addition. A syn elimination is one in which the two groups leave from the same side of the molecule.
Isomers that are rapidly interconverted. For example, enols and ketones are tautomers because they are rapidly interconverted by treatment with either acid or base.
Thermodynamic control
Equilibrium reactions that yield the lowest-energy, most stable products are said to be thermodynamically controlled. Even though it is most stable, the product of a thermodynamically controlled reaction is not necessarily formed fastest.
Torsional Strain
The strain in a molecule caused by electron repulsion between eclipsed bonds. Torsional strain destabilizes boat cyclohexane relative to chair cyclohexane.
Transition state
An activated complex between reagents, representing the highest-energy point on a reaction curve. Transition states are unstable complexes that can not be isolated.
Unimolecular reaction
A reaction that occurs by spontaneous transformation of the starting material without the intervention of other reactants. For example, the dissociation of a tertiary alkyl halide in the SN1 reaction is a unimolecular process.
A molecule that has multiple bonds and can undergo addition reactions. Alkenes and alkynes, for example, are unsaturated.
Van der Waals forces
The attractive forces between molecules caused by dipole-dipole interactions. Van der Waals forces are one of the primary fporces responsible for holding molecules together in the liquid and solid states.
Zaitsev's rule
A rule stating that E2 elimination reactions normally yield the more highly substituted alkene as the major product.
Zusammen (Z)
A term used to describe the stereochemistry of a carbon-carbon double bond. The two groups on each carbon atom are first assigned priorities according to the Cahn-Ingold-Prelog sequence rules, and the two carbons are then compared. If the high-priority groups on each carbon are on the same side of the double bond, the bond has Z geometry. (See Entgegen .)
Version 0.2.5, 09/21/97