The following are definition and terms associated with organic chemistry. It is therefore important for one to get farmiliarized with them. They include;
1. 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.
2. Absorption spectrum: A plot of
wavelength of incident light versus amount of light absorbed. Organic molecules
show absorption spectra in both the infrared and ultraviolet regions of the
electromagnetic spectrum. By interpreting these spectra, useful structural
information about the sample can be obtained.
3.
Acetal: A functional group consisting
of two ether-type oxygen atoms bound to the same carbon, R2C(OR’)2. Acetals are
often used as protecting groups for ketones and aldehydes, since they are
stable to basic and nucleophilic reagents but can be easily removed by acidic
hydrolysis.
4.
Achiral: Having a lack of handedness. A
molecule is achiral if it has a plane of symmetry and is thus superimposable on
its mirror image.
5.
Activating
group: An electron-donating group such as hydroxyl (— OH) or amino (— NH2)
that increases the reactivity of an aromatic ring toward electrophilic aromatic
substitution. All activating groups are ortho- and para directing.
6.
Activation energy: The difference in
energy levels between ground state and transition state. The amount of
activation energy required by a reaction determines the rate at which the
reaction proceeds. The majority of organic reactions have activation energies
of 10—25 kcal/mol.
7.
Acylation: The introduction of an acyl
group, — COR, onto a molecule. For example, acylation of an alcohol yields an
ester (R’OH —, R’OCOR), acylation of an amine yields an amide (R’NH2 —>
R’NHCOR), and acylation of an aromatic ring yields an alkyl aryl ketone (ArH —ArCOR).
8.
Acylium ion: A resonance-stabilized
carbocation in which the positive charge is located at a carbonyl-group carbon,
R—C+= 0 <-* R— C ó. Acylium ions are strongly electrophilic and are involved
as intermediates in Friedel—Crafts acylation reactions.
9.
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.
10.
Aldaric acid: The dicarboxylic acid
resulting from oxidation of an aldose.
11.
Alditol: The polyalcohol resulting from
reduction of the carbonyl group of a sugar.
12.
Aldonic acid : The monocarboxylic acid
resulting from mild oxidation of an aldose.
13.
Alicyclic: Referring to an aliphatic
cyclic hydrocarbon such as acycloalkane or cycloalkene.
14.
Aliphatic: Referring to a nonaromatic
hydrocarbon such as a simple alkane, alkene, or alkyne.
15.
Alkaloid: A naturally occurring
compound that contains a basic amine functional group. Morphine is an example
of an alkaloid.
16.
Alkylation: Introduction of an alkyl
group onto a molecule. For example, certain aromatic rings can be alkylated to
yield arenes (ArH — ArR), alkoxide anions can be alkylated to yield ethers (R’O
— R’OR), and enolate anions can be alkylated to yield alpha-substituted
carbonyl compounds [RC=C(R’)O — RRC—COR’].
17.
Allylic: Used to refer to the position
next to a double bond. For example, CH2 = 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 (C=C—C -* C—C=C).
18.
Angle strain: The strain introduced
into a molecule when a bond angle is deformed from its ideal value. Angle
strain is particularly important in small-ring cycloalkanes, where it results
from compression of bond angles to less than their ideal tetrahedral values.
For example, cyclopropane has approximately 22 kcal/mol angle strain owing to
bond deformations from the 109° tetrahedral angle to 60°.
19.
Anomers: Cyclic stereoisomers of sugars
that differ only in their configurations at the hemiacetal (anomeric) carbon.
20.
Antarafacial: A word used to describe
the geometry of pericyclic reactions. An antarafacial reaction is one that
takes place on opposite faces of the two ends of a pi electron system. (See
Suprafacial.)
21.
Anti conformation: The geometric
arrangement around a carbon— carbon single bond, in which the two largest
substituents are 180° apart as viewed in a Newman projection.
22.
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 Br2 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.)
23.
Antibonding
orbital: A molecular orbital that is higher in energy than the atomic
orbitals from which it is formed.
24.
Anticodon: A sequence of three bases on
tRNA that reads the codons on mRNA and brings the correct amino acids into
position for protein synthesis.
25.
Aromaticity: 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 ‘H NMR spectrum, and a tendency to undergo
substitution reactions rather than addition reactions on treatment with
electrophiles. Aromatic molecules must be planar, cyclic, conjugated species
that have (4n + 2) pi electrons.
26.
Asymmetric center: See Chiral center.
27.
Atactic
polymers: Chain-growth polymers that have a random stereochemical
arrangement of substituents on the polymer backbone. These polymers result from
high-temperature radical-initiated polymerization of alkene monomers.
28.
Aufbau principle: A guide for
determining the ground-state electronic configuration of elements by filling
the lowest-energy orbitals first.
29.
Axial bond: A bond to chair cyclohexane
that lies along the ring axis perpendicular to the rough plane of the ring.
(See Equatorial bond.) Axial bonds
30.
Base peak: The most intense peak in a
mass spectrum.
31.
Bent
bonds: The bonds in small rings such as cyclopropane that bend away from
the internuclear line and overlap at a slight angle, rather than head-on. Bent
bonds are highly strained and highly reactive.
32.
Benzylic: Referring to the position
next to an aromatic ring. For example, a benzylic cation 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.
33.
Benzyne: An unstable intermediate
having a triple bond in a benzene ring. Benzynes are implicated as
intermediates in certain nucleophilic aromatic substitution reactions of aryl
halides with strong bases.
34.
Betaine: A neutral dipolar molecule
that has nonadjacent positive and negative charges. For example, the initial
adducts of Wittig reagents with carbonyl compounds are betaines:
35.
Bimolecular reaction: A reaction that
occurs between two reagents.
36.
Block copolymer: A polymer consisting
of alternating homopolymer blocks. Block copolymers are usually prepared by
initiating chain-growth polymerization of one monomer, followed by addition of
an excess of a second monomer.
37.
Boat cyclohexane: A three-dimensional
conformation of cyclohexane that bears a slight resemblance to a boat. Boat
cyclohexane has no angle strain, but has a large number of eclipsing
interactions that make it less stable than chair cyclohexane:
38.
Bond angle: The angle formed between
two adjacent bonds.
39.
Bond-dissociation
energy: The amount of energy needed to homolytically break a bond to
produce two radical fragments.
40.
Bond length: The equilibrium distance
between the nuclei of two atoms that are bonded to each other.
41.
Bond strength: See Bond-dissociation
energy.
42.
Bonding
orbital: A molecular orbital that is lower in energy than the atomic
orbitals from which it is formed.
43.
Bromohydrin: The 1,2-disubstituted bromoalcohol
that is obtained by addition of HOBr to an alkene.
44.
Brønsted
acid: A substance that donates a hydrogen ion (proton) to a base.
45.
Carbanion: A carbon anion, or a
substance that contains a trivalent, negatively charged carbon atom. Carbanions
are sp3 hybridized and have eight electrons in the outer shell of the
negatively charged carbon.
46.
Carbene: A neutral substance that
contains a divalent carbon atom having only six electrons in its outer shell (R2C:).
47.
Carbinolamine: A molecule that contains
the R2C(OH)NH2 functional group. Carbinolamines are produced as unstable
intermediates during the nucleophilic addition of amines to carbonyl groups.
48.
Carbocation: A carbon cation, or a
substance that contains a trivalent, positively charged carbon atom having six
electrons in its outer shell (R3C+ Carbocations are planar and sp2 hybridized).
49.
Carbocycle: A cyclic molecule that has
only carbon atoms in the ring. (See Heterocycle.)
50.
Carbohydrate: A polyhydroxy aldehyde or
polyhydroxy ketone. The name derives from the fact that glucose, the most
abundant carbohydrate, has the formula C6H1206 and was originally thought to be
a “hydrate of carbon.” Carbohydrates can be either simple sugars such as
glucose or complex sugars such as cellulose. Simple sugars are those that
cannot be hydrolyzed to yield smaller molecules, whereas complex sugars are
those that can be hydrolyzed to yield simpler sugars.
51.
Chain-growth polymer: A polymer
produced by a chain-reaction procedure in which an initiator adds to a
carbon—carbon double bond to yield a reactive intermediate. The chain is then
built as more monomers add successively to the reactive end of the growing chain.
52.
Chain reaction: A reaction that, once
initiated, sustains itself in an endlessly repeating cycle of propagation
steps. The radical chlorination of alkanes is an example of a chain reaction
that is initiated by irradiation with light and then continues in a series of
propagation steps: eg chlorination reaction.
53.
Chair cyclohexane: A 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:
54.
Chemical shift: The position on the NMR
chart where a nucleus absorbs. By convention, the chemical shift of
tetramethylsilane (TMS) is arbitrarily set at zero, and all other absorptions
usually occur downfield (to the left on the chart). Chemical shifts are expressed
in delta units, 6, where 1 6 equals 1 ppm of the spectrometer operating
frequency. For example, 1 6 on a 60 MHz instrument equals 60 Hz. The chemical
shift of a given nucleus is related to the chemical environment of that nucleus
in the molecule, thus allowing one to obtain structural information by
interpreting the NMR spectrum.
55.
Chiral:
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 lefthanded. 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.)
56.
Chiral center: An atom (usually carbon)
that is bonded to four different groups and is therefore chiral. (See Chiral.)
57.
Chlorohydrin: The 1,2-disubstituted
chloroalcohol that is obtained by addition of HOC1 to an alkene.
58.
Chromatography: A technique for
separating a mixture of compounds into pure components. Chromatography operates
on a principle of differential adsorption whereby different compounds adsorb to
a stationary support phase and are then carried along at different rates by a
mobile phase.
59.
Cis—trans
isomers: Special kinds of stereoisomers that differ in their
stereochemistry about a double bond or on a ring. Cis—trans isomers are also
called geometric isomers.
60.
Codon: A three-base sequence on the
mRNA chain that encodes the genetic information necessary to cause specific
amino acids to be incorporated into proteins. Codons on mRNA are read by
complementary anticodons on tRNA.
61.
Concerted: Referring to a reaction that
takes place in a single step without intermediates. For example, the
Diels—Alder cycloaddition reaction is a concerted process.
62.
Configuration:
The three-dimensional arrangement of atoms bonded to a chiral center relative
to the stereochemistry of other chiral centers in the same molecule.
63.
Conformation: The exact
three-dimensional shape of a molecule at any given instant, assuming that
rotation around single bonds is frozen.
64.
Conformational analysis: A means of
assessing the minimum- energy conformation of a substituted cycloalkane by
totaling the steric interactions present in the molecule. Conformational
analysis is particularly useful in assessing the relative stabilities of
different conformations of substituted cyclohexane rings.
65.
Conjugate addition: Addition of a
nucleophile to the p-carbon atom of an a,-unsaturated carbonyl compound. (See
1,4-Addition.)
66.
Conjugate
base: The anion that results from dissociation of a Brønsted acid.
67.
Conjugation: A series of alternating
single and multiple bonds with overlapping p orbitals. For example,
1,3-butadiene is a conjugated diene, 3-buten- 2-one is a conjugated enone, and
benzene is a cyclic conjugated triene.
68.
Conrotatory:
A term used to indicate the fact that p orbitals must rotate in the same
direction during electrocyclic ring opening or ring closure. (See Disrotatory.)
69.
Constitutional isomers: Isomers that
have their atoms connected in a different order. For example, butane and
2-methyipropane are constitutional isomers.
70.
Copolyiner: A polymer formed by
chain-growth polymerization of a mixture of two or more different monomer
units.
71.
Coupling constant: The magnitude
(expressed in hertz) of the spin—spin splitting interaction between nuclei
whose spins are coupled. Coupling constants are denoted J.
72.
Covalent
bond: A bond formed by sharing electrons between two nuclei. (See Ionic
bond.)
73.
Cracking: A process used in petroleum
refining in which large alkanes are thermally cracked into smaller fragments.
74.
Cycloaddition: A pericyclic reaction in
which two reactants add together in a single step to yield a cyclic product.
The Diels—Alder reaction between a diene and a dienophile to give a cyclohexene
is the best-known example of a cycloaddition.
75.
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.
76.
Decarboxylation: A reaction that involves
loss of carbon dioxide from the starting material. /3-Keto acids decarboxylate
particularly readily on heating.
77.
Degenerate orbitals: Two or more
orbitals that have the same energy level.
78.
Dehydration: A reaction that involves
loss of water from the starting material. Most alcohols can be dehydrated to
yield alkenes, but aldol condensation products (/3-hydroxy ketones) dehydrate
particularly readily.
79.
Dehydrohalogenation: A reaction that
involves loss of fiX from the starting material. Alkyl halides undergo
dehydrohalogenation to yield alkenes on treatment with strong base.
80.
Delocalization: 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 stabilization over the entire pi electron system.
81.
Denaturation: The physical changes that
occur in proteins when secondary and tertiary structures are disrupted.
Denaturation is usually brought about by heat treatment or by a change in pH
and is accompanied by a loss of biological activity.
82.
Deshielding: An effect observed in NMR
that causes a nucleus to absorb downfield (to the left) of TMS standard.
Deshielding is caused by a withdrawal of electron density from the nucleus and
is responsible for the observed chemical shifts of vinylic and aromatic
protons.
83.
Deuteriuin isotope effect: A tool for
use in mechanistic investigations to establish whether or not a C — H bond is
broken in the rate-limiting step of a reaction. Since carbon—deuterium bonds
are stronger and less easily broken than carbon—protium bonds, one can measure
the reaction rates of both protiumand deuterium-substituted substrates and see
if they are the same. If they are different, a deuterium isotope effect is
present, indicating that C—H bond breakage is rate-limiting.
84.
Dextrorotatory: A word used to describe
an optically active substance that rotates the plane of polarization of
plane-polarized light in a right-handed (clockwise) direction. The direction of
rotation is not related to the absolute configuration of the molecule. (See
Levorotatory.)
85.
Diastereomer: 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.
86.
Diazotization: The conversion of a
primary amine, RNH2, into a diazonium salt, RN, by treatment with nitrous acid.
Aryl diazonium salts are stable, but alkyl diazonium salts are extremely
reactive and are rarely isolable.
87.
Dielectric constant: A measure of the
ability of a solvent to act as an insulator of electric charge. Solvents that
have high dielectric constants are highly polar and are particularly valuable
in 5N1 reactions because of their ability to stabilize the developing positive
charge of the intermediate carbocation.
88.
Dienophile: A compound containing a
double bond that can take part in the Diels—Alder cycloaddition reaction. The
most reactive dienophiles are those that have electron-withdrawing groups such
as nitro, cyano, or carbonyl on the double bond.
89.
Bipolar aprotic solvent: Dipolar
solvent that cannot function as a hydrogen ion donor. Dipolar aprotic solvents
such as dimethyl sulfoxide (DMSO), hexamethylphosphoramide (HMPA), and
dimethylformamide (DMF) are particularly useful in 5N2 reactions because of
their ability to solvate cations.
90.
Dipole
moment, z: A measure of the polarity of a molecule. A dipole moment arises
when the centers of gravity of positive and negative charges within a molecule
do not coincide.
91.
Disrotatory: A term used to indicate
the fact that p orbitals rotate in opposite directions during electrocyclic
ring opening or ring closing. (See Conrotatory.)
92.
d,l
form: A shorthand way of indicating the racemic modification of a compound.
(See Racemic mixture.)
93.
DNA:
Deoxyribonucleic acid, the biopolymer consisting of deoxyribonucleotide units
linked together through phosphate—sugar bonds. DNA, which is found in the
nucleus of cells, contains an organism’s genetic information.
94.
Doublet: A two-line NMR absorption
caused by spin—spin splitting when the spin of the nucleus under observation
couples with the spin of a neighboring magnetic nucleus.
95.
Downfield: Refers to the left-hand
portion of the NMR chart. (See Deshielding.)
96.
Eclipsed conformation: The geometric
arrangement around a carbon—carbon single bond in which the bonds to
substituents on one carbon are parallel to the bonds to substituents on the
neighboring carbon as viewed in a Newman projection. For example, the eclipsed
conformation of ethane has the C — H bonds on one carbon lined up with the C H
bonds on the neighboring carbon:
97.
Eclipsing strain: The strain energy in
a molecule caused by electron repulsions between eclipsed bonds. Eclipsing
strain is also called torsional strain.
98.
Elastomers:
Amorphous polymers that have the ability to stretch out and then return to
their previous shape. These polymers have irregular shapes that prevent
crystallite formation and have little cross-linking between chains.
99.
Electrocyclic reaction: A unimolecular
pericyclic reaction in which a ring is formed or broken by a concerted
reorganization of electrons through a cyclic transition state. For example, the
cyclization of 1,3,5-hexatriene to yield 1,3- cyclohexadiene is an
electrocyclic reaction.
100.Electromagnetic spectrum: The range of
electromagnetic energy, including infrared, ultraviolet, and visible radiation.
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