1

Stereochemistry
• Definition: “Stereochemistry refers to the 3-dimensional properties and
reactions of molecules.” OR “ It is the study of the static and dynamic aspects
of the three-dimensional shapes of molecules.”

• The field of stereochemistry is one of the central parts of organic chemistry

and includes many important topics. It provides a foundation for
understanding structure and reactivity.

Contents:

• Isomerism
• Stereoisomerism
• Optical isomerism
• Geometrical isomerism
• Molecules with more than one chiral center
• Resolution of racemic mixture 2
 Isomerism
• Isomerism: “Two or more than two compounds having same molecular
formula (due to similar number of atoms of each element in them) but
different structures (due to different attachments or arrangements of atoms)
are known as isomers and the phenomenon of formation or existence of
isomers is called isomerism.”

• Isomers: Isomers are different compounds with the same molecular formula.
"Iso" means "same" & "mers" means "parts".
Note: Isomers differ in physical and chemical properties.

Basic two types of isomerism:

1. Constitutional or Structural Isomerism: “Structural isomerism, or
constitutional isomerism (as per IUPAC), is a form of isomerism in which
molecules with the same molecular formula have a different connectivity or
different bonding patterns and atomic organization.”
2. Stereoisomerism: “Stereoisomerism is a form of isomerism in which each of
two or more compounds with the same molecular formula differ only in the
configuration i.e. spatial or three-dimensional arrangement of their atoms.” 3
 Comparison of Constitutional Isomers and Stereoisomers

Constitutional isomers have:

• different IUPAC names;
• the same or different functional groups;
• different physical properties, so they are separable by physical techniques such as
distillation; and different chemical properties.
• They behave differently or give different products in chemical reactions.

Stereoisomers differ only in the way atoms are oriented in space. 4

Are the Following Pairs of compounds consitutional
isomers or stereoisomers ?

a) constitutional

b) constitutional

c) stereoisomer

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6
 [A]. Structural or Constitutional Isomerism
• Definition: “Constitutional/structural isomers are the compounds having same
molecular formula but different structural formulas and the phenomenon of their
formation or existence is known as structural or constitutional isomerism.”

• By “different structural formulas” we mean that they differ in the kinds of bonds
(single, double or triple) and/or in the connectivity of their atoms. These are the
isomers having different IUPAC names, the same or different functional groups,
different physical properties and different chemical properties.
• E.g. Butane and 2-methylpropane. They are different compounds having different
physical and chemical properties. Their boiling points, for example, differ by
approximately 11°C.

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Types of Structural Isomerism:

[1]. Chain isomerism: “When two or more compounds have similar molecular
formula but different carbon skeletons (chains), they are referred to as chain
isomers and the phenomenon of their formation or existence is termed as
chain isomerism.”

• For example, C5H12 represents three compounds:

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[2]. Position Isomerism: “When two or more compounds having same
molecular formula differ in the position of the same substituent atom or
functional group on the carbon skeleton, they are called position isomers
and the phenomenon of their formation or existence is termed as position
isomerism.”

For example, the molecular formula C3H8O represents two alcohols.

Similarly, Propyl chloride and isopropyl chloride are the positional isomers
with the molecular formula, C3H7 Cl.

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[3]. Functional group isomerism: “Two or more compounds having the same
molecular formula but different functional groups are called functional group
isomers and the phenomenon of their formation or existence is termed as
functional group isomerism.”

For example, the molecular formula C3H6O represents an aldehyde and a

ketone.

Similarly, Dimethyl ether is a functional group isomer of ethyl alcohol. Both

have the same molecular formula, C2H6O. However they have different
functional groups.

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• “Tautomerism refers to the dynamic equilibrium between two compounds
with same molecular formula.”

• It is most often a special case of functional group isomerism. In general,

the tautomers have different functional groups and exist in dynamic
equilibrium with each other due to a rapid interconversion from one form
to another.

Example of Keto-enol tautomerism:

• The carbonyl compounds containing at least one α-hydrogen atom exhibit

keto-enol tautomerism. The carbonyl group can be converted to enol form
due to transfer of one of the α-hydrogen onto the oxygen atom.

• Note: An alcoholic group on C=C is called enol. It is an alkene alcohol.

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• The % composition of keto enol tautomeric mixture depends on the relative
stabilities of these two forms.

• In general the keto form is the low energy form and is more stable than the
enol form. However the enol form is also stable in certain cases due to other
stability factors.

• The dynamic equilibrium between a keto form and an enol form exhibited
by acetone is shown below.

• The tautomers are formed due to complete transfer of a hydrogen atom.

However the relatively stable keto form exists in higher percentage (about
99%).

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[4]. Metamerism: “Two or more molecules having same molecular formula
and same multivalent functional group but different number of carbon
atoms (alkyl groups) attached to either side of the functional group, are
known as metamers and the phenomenon of their formation or existence is
known as metamerism.”

• Important Condition: Metamerism is shown only by those molecules whose

functional group is multivalent i.e., which can make more than one bonds.

• So either ethers (ROR) or ketones (RCOR) or esters (RCOOR) can show the
phenomenon of metamerism, because all of them have a multivalent
functional group.

• For example, C4H10O represents methyl propyl ether (or 1-

methoxypropane), isopropyl methylether (or 2-methoxypropane) and
diethyl ether (or ethoxyethane). All are metamers.

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[5]. Ring Chain Isomerism: “Open chain and cyclic
compounds having the same molecular formula are
called ring-chain isomers and the phenomenon of
their formation or existence is termed as ring-chain
isomerism.”

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 [B]. Stereoisomerism
• Definition: “Compounds having same molecular formula, same
constitution and same sequence of covalent bonds but differ in the three-
dimensional orientations i.e. relative positions of their atoms or groups in
space are called stereoisomers and the phenomenon of their formation or
existence is called as stereoisomerism.”

• Sterioisomers have identical IUPAC names except for a prefix like cis or
trans, L or D etc. Because they differ only in the three dimensional
arrangement of atoms (called a configuration), stereoisomers always have
the same functional group(s).

Types of Stereoisomerism:

Stereoisomerism is of two types:

1. Configurational Isomerism
2. Conformational Isomerism
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[1]. Configurational Isomerism:
• Definition: “Stereoisomers which cannot be interconverted unless a
covalent bond is broken are called configurational isomers or simply
configurations and the phenomenon of their formation or existence is called
as configurational isomerism.”

• The configurational isomerism is again of two types:

A. Geometrical Isomerism
B. Optical Isomerism or Enantiomerism

[A]. Geometric Isomerism (also known as cis-trans isomerism or E-Z

isomerism):
Definition: "Two or more than two compounds having same molecular
formula and same structural formula but due to restricted rotation across a
double bond or a ring structure have a different spatial geometry (i.e.,
arrangement of its atoms or groups of atoms in space) are known as
Geometric or Cis-Trans isomers and the phenomenon of their formation or
existence is known as Geometric or Cis-Trans Isomerism.” 16
• Geometric Isomerism results most commonly from carbon-carbon double
bonds i.e. in alkenes mainly. The important property which introduces the
feature is the inability of the carbon atoms to rotate relative to one another
about the double bond. Because rotation will break the double bond. This is
due specifically to the Pi bond.

• Cis isomer is one in which two similar groups are on the same side of a double
bond.
• Trans isomer is that in which two similar groups are on the opposite side of
the double bond.

• Trans isomers are more stable than the corresponding cis isomer. This is
because in trans bulky groups are on the opposite side, hence less repulsion or
steric hindrance. The alkyl group attached with the double bonded carbon
atom of an alkene is known as "bulky group".

• Geometrical isomers have different physical and chemical properties. These

can be separated by conventional techniques like distillation, gas
chromatography etc.
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• Example: Consider the case of 2-butene. It exists in two special
arrangements i.e. Cis 2-butene and Trans 2-butene.

• Conversion of such isomers into each other is only possible if heated at high
temperature or absorb light. Energy around 62 Kcal/mole is needed.

• Geometrical isomerism in cyclic compounds: Geometrical isomerism is

possible in cyclic compounds as well. There should be restriction of rotation
if two carbons are linked with a cyclic structure. Example No. 1:

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Example No. 2: Cis and trans isomers are also possible for 1,4-
dimethylcyclohexane.
Stereocenter or
Stereogenic Centre:
According to new
concept “It is a
tetrahedral atom, most
commonly carbon, at
which exchange of two
groups produces a
stereoisomer.”
E.g. 1,2-dimethylcyclopentane has two stereocenters i.e. both carbons 1 and
2. In this molecule, exchange of H and CH3 groups at either stereocenter
converts a trans isomer to a cis isomer, or vice versa.

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• Old Concept of Stereogenic Centre: “It is a tetrahedral atom, most
commonly carbon, to which four different ligands or groups are attached.”
• Note: Its new name is assymmetric centre/carbon or chiral centre/carbon.

• E.g.:

Molecules can contain zero, one, or more stereogenic centers.

1. With no stereogenic centers, a molecule generally is not chiral. H2O and
CH2BrCl have no stereogenic centers and are achiral molecules.
2. With one or more stereogenic centers, a molecule is always chiral.
CHBrClF is a chiral molecule containing one stereogenic center.
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[B]. Optical Isomerism (Enantiomerism): “Optical isomerism is a type of
stereoisomerism in which the isomers are identical in molecular weight and most
chemical and physical properties but differ in their effect on the rotation of the plane
of polarized light.”
• In optical isomers, asymmetry of the molecule as a whole or the presence of one
or more asymmetrical atoms is responsible for such effects.

• These molecules are not necessarily locked into their positions, but normally
cannot be converted into one another, even by a rotation around a single bond.
E.g. Molecular formula C3H6O3 represents two enantiomeric lactic acids as shown
below:

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Concept of Enantiomers and Diastereomers:
[1]. Enantiomers: “When two chiral stereoisomers are non-congruent (non-
superimposable) mirror images of each other, they are known as
enantiomers.”

Enantiomers have identical chemical and physical properties (IR, NMR, m.p,
mass spectra, etc.), except for their ability to rotate plane polarized light (+/-)
by equal amounts but in opposite directions. Examples:

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[2]. Diastereomers:
“Diastereomers are stereoisomers that are not enantiomers i.e. that are not mirror
images of eachother.” Diastereomers can have different physical properties and
reactivity. They have different melting points and boiling points and different
densities. They have two or more stereocenters.

• Notice that a is the mirror image of b, and C is the mirror image of d. Thus, four
isomers are two pairs of enantiomers. Now, compare a and c. They are neither
super imposable nor are they mirror images they are called
as diastereomers. Thus, a and C and b and d etc. are diastereomers. So, stereo
isomers, which are not mirror images are called diastereomers.

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Enantiomers and Diastereomers

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 For Your Concept

Figure: Simple flowchart for

classifying various kinds of
isomers.

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[2]. Conformational Isomerism:
• Definition: “The stereoisomers which can be interconverted simply by
rapid rotation (twisting) about one or more single bonds (σ bonds) at room
temperature without breaking the covalent bond are called conformational
isomers (or conformers or rotational isomers or rotamers) and the
phenomenon of their formation is known as Conformational Isomerism.”

• Conformers interconvert rapidly so they cannot be separated under normal

conditions and therefore have a structure which is an average of
conformers.

• Conformation: The shapes that a molecule can adopt due to rotation

around one or more single bonds are called conformations.

• Two types of conformational isomers are:

a) Conformational isomers resulting from rotation about single bond.
b) Conformational isomers arising from amine inversion.
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(a). Conformational Isomers Resulting from Rotation About
Single Bond:
• Because the single bond in a molecule rotates continuously, the
compounds containing single bonds have many inter-convertible
conformational isomers .
• Example: 'boat' and 'chair' forms of cyclohexane.

• Conformational isomers are normally best seen using Newman

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• Example of Butane: Eclipsed, gauche, and anti butane are all conformational
isomers of one another.

• (Eclipsed means that identical groups are all directly in-line with one
another, gauche means that identical groups are 60 degrees apart from one
another, and anti means that identical groups are at 180 degrees from one
another).

• These molecules can be interconverted by rotating around the central carbon

single bond. For example, eclipsed butane can be made into gauche butane by
rotating 60 degrees and into anti butane by rotating 180 degrees. Similarly, gauche
butane can be made into anti butane by rotating 120 degrees. This rotation can be
seen below.

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• Because of this rotational property, eclipsed, gauche, and anti butane
(b) Conformational Isomers Arising from Amine Inversion:
• Nitrogen atom of amines has a pair of non-bonding electrons which allow the
molecule to turn "inside out" rapidly at room temperature. This is called amine
inversion or Walden inversion.
• Example: Nitrogen inversion interconverts the two enantiomers of a simple chiral
amine like ethylmethylamine. Resolution of amines is difficult because nitrogen
inversion interconverts the enantiomers.

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A Review of Isomerism

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Important Detail Related to Optical Isomerism
• Asymmetric Atom or Asymmetric Center: It is an sp3 carbon atom (mostly)
with 4 different groups attached. It is also called as chiral center.

• Optically active molecules are those that can rotate the plane of polarized
light.
• Note: The result of interaction of plane-polarized light with a chiral
compound is rotation of the plane of polarization.

• Chiral Compound: A compound is said to be chiral if it contains a chiral

center. Molecules of most chiral compounds contain one or more
stereogenic centers.

• ‹Ordinary light: Light oscillating in all planes perpendicular to its direction

of propagation.

• ‹Plane-polarized light: Light oscillating only in parallel planes.

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 Ordinary and Plane-Polarized Light

normal light plane-polarised light plane-polarised light after

(waves vibrate in all directions) (vibrates in only one direction) clockwise rotation

(-)-enantiomer (+)-enantiomer (±)-racemate

(anticlockwise rotation) (clockwise rotation) (no overall effect)
 Plane-Polarized Light through a Chiral Compound
• Optical isomers rotate the plane of plane polarised light.

• Optical rotation is an inherent property of an optically active compound and is

used as a physical constant for characterization of the compound.

• Optical rotation depends on the arrangement of atoms or groups around the chiral
center—the configuration.

• Optical activity is measured automatically with an instrument called a polarimeter.

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 Plane-Polarized Light through an Achiral Compound

Polarimetry: It is a sensitive, nondestructive technique for measuring the

optical activity exhibited by inorganic and organic compounds.

• Historically, the most common technique used to detect chirality and to

distinguish enantiomers has been to determine whether a sample rotates
plane polarized light. 34
 Polarimeter
• Polarimeter: “A device for measuring the extent of rotation of plane-
polarized light.” OR “An instrument that measures the optical rotation of the
chiral compound.”
• Polarimeters can be used to analyse the effect that optical isomers have on
plane polarised light.

A B
C D
E
F

A Light source produces light vibrating in all directions

B Polarising filter only allows through light vibrating in one direction
C Plane polarised light passes through sample
D If substance is optically active it rotates the plane polarised light
E Analysing filter is turned so that light reaches a maximum
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F Direction of rotation is measured coming towards the observer
Polarimeter

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Measurement of Optical Rotation: We can measure optical rotation, the direction and the
degree (angle) of rotation by using a polarimeter.

1. Ordinary light vectors (lines) oscillate randomly (in all directions); it is symmetrical. When
ordinary light is passed through a polarizer like Nicol prism, only the light whose electric
and magnetic vectors oscillate in one specific direction (plane) can pass. The light so becomes
plane polarized light.

2. When plane polarized light passes through a solution of chiral molecules the plane of
polarization is rotated by a certain angle in a certain direction, either clockwise or counter-
clockwise (that’s why chiral compounds are said to be optically active).

3. Compounds that rotates light clockwise (towards right) are called dextrorotatory (dexter is
Greek word that means “right”); they are designated by a prefix of (+) or d before their names.
Compounds that rotate light to the left (anticlockwise) are called levorotatory (Greek for left);
they are designated by a (–) or letter l in front of their names.

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Factors Affecting Angle of Rotation:
(1). The measured angle of rotation, α, depends on several factors, including the
type of molecule and the number of molecules in the light path; this quantity is
given by concentration, c, of the chiral substance and

(2). the distance light travels through the solution, the cell length, l.

Other factors include (3). the temperature and (4). wavelength of the polarized
light.

We combine these factors in defining the specific rotation, [α], which is the
observed rotation of an optically active substance in a solution at a
concentration of 1.0 g/mL, and a path length, l = 1.0 dm (10 cm).

OR The number of degrees by which an optically active compound rotates the

plane of polarized light is called its specific rotation and is given the symbol [α].
The specific rotation is calculated
from the measured rotation, α, as
follows: 38
• The temperature (T) and wavelength (λ) are indicated by superscripts and
subscripts, respectively.

• It is common practice to report the temperature (in °C) at which the

measurement is made. The most common wavelength of light used in
polarimetry is the sodium D line i.e., 589 nm, the wavelength responsible for
the yellow color of sodium-vapor lamps.

Absence of Optical Activity:

• When we detect optical activity, we can be sure that a chiral compound is
present. But, failure to observe optical activity does not always mean that no
chiral compound is present.
• Each compound with an asymmetric C-atom has two enantiomers, each
rotating light with the same magnitude of specific rotation, but rotating
light in opposite directions, one to the right (+) and one to the left (–).

• If we have a 50-50 mixture of the pair of enantiomers, we observe NO

rotation at all, because the two rotations, equal in magnitude but opposite in
direction, cancel each other. 39
 Important Stereochemical Terminology
[1]. Epimers: “Epimers are those diastereomers that differ in configuration at
only one centre of chirality.” They have the same configuration at all other
stereogenic centres.

[2]. Epimerization: The interconversion of epimers i.e. the process of changing

the absolute configuration at one of the stereogenic centers of a diastereomer is
called Epimerization.

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41
[3]. Prochiral Molecule: A molecule that is achiral but that can become chiral
by a single alteration is a prochiral molecule.

[4]. Relative configuration: “This refers to the configuration of any stereogenic

center with respect to another stereogenic center.” If one center in a molecule
is known as R, then other centers can be compared to it using the descriptors
R*or S*, indicating the same or opposite stereochemistry, respectively.

[5]. Enantiopure Compounds: “Enantiopure compounds refer to the samples

having, within the limits of detection, molecules of only one chirality i.e.
comprising of a single stereoisomer only.”

• Note: Enantiopure compounds are often expensive. 42

[6]. Meso compounds, or meso forms: “In the simplest case, a compound
with two chirality centers where there is the same set of four groups at each
chirality center, and these four groups are arranged such that the centers are
mirror images of each other (i.e., the molecule has an internal mirror plane
or plane of symmetry) is a meso compound.”

Note: Meso compound is achiral and optically inactive.

[7]. Optical Activity: “It is the ability of chiral substances to rotate the plane of
polarized light by a specific angle.” In order for a sample to be optically active,
it must have an excess of one enantiomer. Note: Optical activity establishes
that a sample is chiral, but a lack of optical activity does not prove a lack of
chirality.
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[8]. Specific Rotation: “It is the measured angle of rotation of polarized light by a
pure chiral sample under specified standard conditions.”

[9]. Chirality: It is a general property of objects and means that an object is non-
congruent (not superimposable) to its mirror image. An example of a pair of chiral
objects is the human hands. If an object is not chiral—that is, if its mirror image is
congruent with the original—it is achiral.

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[10]. Chiral: The word chiral comes from the Greek word, cheir, which means hand.
Our hands are mirror images of one another, but can’t be superimposed on each
other.

[11]. Chiral center: “Chiral center or chiral carbon is defined as an atom or

specifically carbon, that has four different ligands attached.” Here, the term
‘‘ligand’’ refers to any group attached to the carbon, such as H, R, Ar, OH, etc.
The particular case of a carbon with four different ligands has also been termed an
asymmetric carbon.

[12]. Homochirality: It refers to the property of a group of molecules that possess

the same chirality. It is an important feature of earthly biochemistry. All life on Earth
is homochiral (with rare exceptions); only L-amino acids are encoded in proteins,
and only D-sugars form the backbones of DNA and RNA.

[13]. Chiral and Achiral Molecules: Molecules that exhibit optical activity are said to
be chiral.
Achiral molecules usually contain a plane of symmetry and their mirror images are
superimposable.
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[14]. Asymmetric Carbon: “An asymmetric carbon atom (chiral carbon) is a
carbon atom that is attached to four different types of atoms or groups of
atoms.”

Note: Symmetric molecules are achiral.

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[15]. Plane of symmetry: An imaginary mirror plane passing through an object
dividing it so that one half is the mirror image of the other half. The presence of a
plane of symmetry makes a molecule achiral.

[16]. Chiral pool: “All the chiral compounds found in nature that are readily
accessible to synthetic chemists for the construction of more complex molecules are
referred to as the chiral pool.”

[17]. Observed rotation: The number of degrees, α, through which a compound

rotates the plane of polarized light is called observed or measured rotation.”

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[18]. Enantiomeric excess (ee) is defined as “the absolute difference between
the mole fraction of each enantiomer. OR It is the degree of excess of one
enantiomer over the other in a mixture. ” It is a measurement of purity used for
chiral substances.
[R] - [S]
Enantiomeric excess (ee) = x 100 = %R - %S
[R] + [S]
R and S are the respective fractions of enantiomers in a mixture and R + S = 1 and
ee = %R - %S = % of one enantiomer - % of the other enantiomer

Consider the following example: If a sample mixture contains 75% of one enantiomer
and 25% of the other, the enantiomeric excess is 75% - 25% = 50%. Thus, there is a
50% excess of one enantiomer over the racemic mixture.

[19]. % Optical Purity: The % optical purity of a mixture of enantiomers is given by:

% Optical purity of sample = 100 x (specific rotation of sample mixture) / (specific

rotation of a pure enantiomer).
[ ]sam ple
Percent optical purity = x 100
[ ]pure enantio mer
48
• Note: "optical purity" or "enantiomeric excess (ee)" of a sample of a mixture of enantiomers mean
the same thing.

• A racemic mixture has an ee of 0%, while a single completely pure enantiomer has an ee of 100%.

[20]. Fischer Projections: The use of two-dimensional representations to show the configuration of
molecules with multiple chiral centers are called Fischer projections.

• The horizontal lines represent bonds directed outward toward the observer. The vertical lines
represent bonds directed away from the observer.

• To draw a mirror image of a Fischer projection, simply exchange the left and right positions, whilst
keeping the top and bottom unchanged. Fischer projections are very useful to determine if a
compound is chiral or achiral.

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 Molecules With More Than One Chiral Center
• A molecule may contain not only one, but several chirality centers. Compounds
with n chirality centers may form up to 2n stereoisomers, as each asymmetric
carbon can represent two different absolute configurations.

• The maximum number of combinations of absolute configurations in a molecule,

containing a certain number of chirality centers, can be calculated, regardless of
the structure. A molecule that contains two asymmetric carbons can form up
to 22 = 4 stereoisomers.

• According to the CIP (Cahn-Ingold-Prelog R/S) nomenclature, these configurations

are termed (R) and (S).
• Example: Eight combinations of absolute configurations are possible in a molecule
with three asymmetric carbons (chirality centers) i.e.

RRR all R
RRS, RSR, SRR two R, one S

SSR, SRS, RSS one R, two S

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SSS all S
 Example-1: 2,3-Dibromopentane contains two asymmetric carbons, namely C2 and C3.
As a result, the four possible combinations of absolute configurations are (2S, 3S),
(2R, 3R), (2S, 3R), and (2R, 3S).
All 2,3-dibromopentane stereoisomers are optically active and are two pairs of entantiomers.
Pair of enantiomers A.
Isomeric relationship among the four
stereoisomers of 2,3-dibromopentane.

Pair of enantiomers B.

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 Example-2 of Molecule With More Than One Chiral Center:
As we know that,

 For a molecule with 1 chiral center, 21= 2 stereoisomers are possible.

 ‹For a molecule with 2 chiral centers, a maximum of 22= 4 stereoisomers
are possible.
 ‹For a molecule with n chiral centers, a maximum of 2n stereoisomers are
possible.
 For 2,3,4-trichlorohexane, n = 3; 2n = 8 stereoisomers are possible
CH3 CH3 CH3 CH3
S H Cl Cl H R H Cl Cl H
S H Cl Cl H R H Cl Cl H
RH Cl Cl H S Cl H H Cl
Cl CH2CH3 CH2CH3 CH2CH3 CH2CH3

* * * CH3 CH3 CH3 CH3

H Cl Cl H Cl H H Cl
Cl Cl H Cl H Cl Cl H
Cl H
3 asymmetric centers
H Cl Cl H H Cl Cl H
2n, n= # asymmetric centers (3)
CH2CH3 CH2CH3 CH2CH3 52 CH
CH
8 stereoisomers 2 3
 Biological Importance of Sterioisomerism
Nature is inherently chiral because the building blocks of life (α-amino acids,
nucleotides and sugars) are chiral & appear in nature in enantiomerically pure forms.
[1]. Amino Acids: They are generally homochiral—all amino acids have the same
sense of chirality (left Handed or L).
• There are twenty common amino acids, and all except glycine are chiral. Amino
acids have a central carbon, called an α-carbon, bonded to an NH2 group and a
COOH group.
• 18 of the 19 α-carbons of amino acids have the R configuration, one has the S
configuration.
[2]. Sugars: All sugars have the same sense of chirality (Right handed or D). As the
receptor sites are chiral, (+)-glucose is metabolized by animals but NOT (-)-glucose.
[3]. Enzymes: The chirality of the amino acids leads to chiral enzymes, which in turn
produce chiral natural products.

53
 Pharmaceutical Importance of Sterioisomerism
• Any synthetic substance (drug) to interact with or modify nature are
interacting with a chiral environment.

• This is an important issue for bio-organic chemists, and a practical issue for
pharmaceutical chemists.

• The Food and Drug Administration (FDA) now requires that drugs be
produced in enantiomerically pure forms, or that rigorous tests be
performed to ensure that both enantiomers are safe.

• Many drugs are optically active, with one enantiomer only having the
beneficial effect.

• In the case of some drugs, the other enantiomer can even be harmful, e.g.
thalidomide.

• The conversion of one enantiomer into a racemic mixture is called

racemization. 54
• Example No. 1, Thalidomide: Thalidomide occurs as a racemic mixture.

• The S isomer is a sedative and has teratogenic side effects.

• The R isomer is also a sedative but has no teratogenic activity. However,

the enantiomers are converted into each other in vivo.

• Dosing with a single-enantiomer form of the drug will still lead to both the S
and R isomers eventually being present in the patient's serum and thus
would not prevent adverse effects.

(R)(+) Thalidomide (S)(-) Thalidomide

O O H O O H
H N N
H
N O N O

O O
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a sedative and hypnotic a teratogen
Example No. 2: Many natural compounds such as enzymes are not
symmetrical. Thus individual enantiomers will react with enzymes to give
different results. As is the case of epinephrine given below:

56
• For proper actions, binding of drugs to receptor needs to be properly
matched sterio-chemically at receptor sites.

57
• Example No. 3: One enantiomer of a drug may effectively treat a disease
whereas its mirror image may be ineffective or toxic e.g. Naproxen.

• Example No. 4: L-dopa is more

rapidly absorbed than its
enantiomer D-dopa.

• Example No. 5: A large number

of chiral drugs, however, are sold
as racemic mixtures. The popular
analgesic ibuprofen is an
example.

58
 Resolution of Racemic Mixture
• ‹‹Resolution of Racemic Mixture (Optical Resolution): “The resolution of
racemates or racemic mixture is the separation of an equimolar mixture of
enantiomers (racemate) into its individual component enantiomers by
physical, chemical or bio-chemical methods.”

• Racemic Mixture OR Racemic Modification OR Racemate: “A mixture

consisting of equal amounts (50:50) of an optically active isomer and its
enantiomer is termed as racemic mixture, racemic modification, or racemate.”

• Because a racemic mixture contains equal numbers of dextro-rotatory and

levo-rotatory molecules, it exhibits no optical activity i.e. its specific rotation is
zero and so it does not rotate plane polarized light because the activities of the
individual enantiomers are equal and opposite in value, thereby canceling each
other out.
• Secondly, safety will not be ensured until the elimination of the toxic
enantiomer. Thus enantiomers must be separated in order to observe the
optical activity and to produce optically pure and safe active drugs. 59
• Enantiomers have identical physical properties, and consequently cannot be
directly separated by conventional methods such as distillation, crystallization,
sieving, or chromatography on conventional stationary phases.

• Diastereomers have different physical properties like b.p, m.p, density,

refractive index, solubility etc., so can be separated through conventional
means (distillation, recrystallization, chromatography etc.).

Necessary Condition for Distinguishing Enantiomers:

• Enantiomers are distinguishable if and only if they are placed in a chiral
environment, and all methods to separate or characterize enantiomers are
based on this principle.

• Suppose, for example, that we have a collection of right- and left-handed

gloves, and we want to take out only the right-handed ones. Using a simple
hook to reach into the pile will not be fruitful because a hook is achiral—it
cannot distinguish handedness.

• A chiral object, however, like a right hand, can distinguish between the gloves
60
Resolving Agent:
• “A chiral probe or resolving agent is a chiral compound used to reversibly separate
components of a racemate (racemic mixture) by making a derivative of each
enantiomer that is free of its enantiomer.”
• Enantiomers have the same physical properties, but they differ in a chiral sense, so
a chiral probe must be used for such a separation.
• Any optically pure chiral organic acid or base may be a candidate as resolving
agent.

Characteristics of an Ideal Resolving Agent:

1. It should be a strong acid or base to secure formation of stable salts with
weakly basic or acidic racemates, respectively.
2. The center of chirality should be as close as possible to the functional group
involved in salt formation to provide significant differences in the
stereostructure of the diastereomeric salts.
3. Both enantiomers should be available.
4. It should be chemically stable and should not racemize under the conditions of
resolution.
5. It should be non-toxic, readily recoverable and starting materials for its
preparation should be readily available and inexpensive. 61
Various methods
and techniques for
the separation of
enantiomers exists,
though not all
methods are
equally applicable
for every racemic
mixture.

For each method,

several advantages
and disadvantages
prevail, depending
upon factors such
as time, purity,
chemical
processing, and
inherent side
reactions.
62
 [1]. Chemical Resolution
mixture of 2
diastereomers

react or somehow associate with: (R)-compound X (R)-compound Y

(R)-compound X

(S)-compound X (R)-compound Y (S)-compound X (R)-compound Y

Separate by some technique (chromatography,

Single crystallization, distillation, etc.)
racemic mixture enantiomer
of enantiomers

(S)-compound X (R)-compound Y (R)-compound X (R)-compound Y

single single
diastereomer diastereomer
somehow remove compound Y

(S)-compound X (R)-compound X

single single 63
enantiomer enantiomer
[1]. Chemical Resolution:
• It is a typical procedure for the resolution of chiral compounds. Here we react the
racemic mixture with an enantiomerically pure compound.

• This gives rise to a pair of diastereomers – which have different physical properties
and therefore can be separated based on their differing solubility or via suitable
chemical reaction.
• The resolving agent is then cleaved off, leaving pure separated enantiomers.

Example:
• Alcohols react with the enantiomerically pure tartaric acid, to give two
diastereomeric esters.
• These diasteromeric derivatives can be separated by conventional separation
methods such as crystallization, or chromatography on silica or other conventional
stationary phases.
• After separation of the diastereomers, acid hydrolysis cleaves each ester back to an
optically active alcohol and carboxylic acid.
• The enantiomerically pure resolving agent (tartaric acid) is recovered and often
recycled.
64
65
[2]. Chiral Chromatography:
• “Chiral Chromatography is a branch of chromatography that is oriented towards
the exclusive separation of chiral substances by the use of chiral phases.”

• It is a variant of column chromatography in which the stationary phase contains a

single enantiomer of a chiral compound rather than being achiral.

• The two enantiomers of the same analyte compound differ in affinity to the single-
enantiomer stationary phase and therefore they exit the column at different times.

• For the smaller scales associated with the research laboratory, it is increasingly
becoming the method of choice for analyzing and separating mixtures of
enantiomers.

• The mobile phase can be a gas or liquid giving rise to chiral gas chromatography
and chiral liquid Chromatography.

• Chiral selectivity is usually achieved by employing chiral stationary phases,

although, in chiral liquid chromatography, chiral mobile phases have been
successfully employed. 66
• Example: The most common method for the enantiomeric resolution of ibuprofen
enantiomers and chiral materials in general is high performance liquid
chromatography (HPLC). Chromatography is often much faster and more efficient
than crystallization.

• Two important techniques employed for the direct separation of enantiomers by

chromatography on chiral stationary phases include:
1. Construction of a chiral stationary phase or
2. Prederivatization of the individual enantiomers to produce the diastereisomeric
pair.
• In most instances ethyl chloroformate is used to couple a chiral ligand to the
racemic enantiomers in order to produce the diastereoisomeric pair.
• The most successful chiral packing materials comprise the derivatives of cellulose,
amylose, cyclodextrins, proteins, and amino acids.

67
68
[3]. Bio-Resolution:
• It was introduced by Pasteur in 1858. This method is based on fact that when
certain micro organisms like bacteria, fungi, yeast, moulds, etc. are grown in
dilute solution of racemic mixture, they eat up one enantiomer rapidly than
other.
• If the microorganism is wisely chosen, the desired enantiomer is the only thing that
remains and can then be separated from the mixture by common separation
techniques.

• Example No. 1: The mould Penicillium glaucum preferentially destroys the (+)
isomer of racemic ammonium tartarate leaving (-) ammonium tartarate in
solution.
• Example No. 2: Enzymes are chiral catalysts which often exhibit very high
selectivity for one enantiomer of a racemic mixture.
• Though not exclusively, one enantiomer in general "fits" better on the active site
and is therefore converted to its corresponding ester at a higher rate.
• A continuous process has been described for the enantiospecific hydrolysis of the
ethoxyethyl ester of naproxen using a column packed with Candida cylindracea
immobilized on an ion exchange resin.
• (S)-naproxen is prepared by enzymatic hydrolysis of these racemic esters. 69
• The advantage of the enzymatic method is the high enantiomeric excess, resulting
from the inherent selectivity of the enzyme. The enzyme is reusable and the
products of the reaction are easy to separate.
• The disadvantages of this method are related to the number of parameters that
must be optimized for the enzyme and the selectivity of the system is limited by
the extent of conversion.

70
[4]. Physical/Mechanical Separation Methods:

• This method was first used successfully by Louis Pasteur for the resolution
of sodium ammonium tartarate which crystallise out in the form of racemic
mixture below 27 degree.

• This involved mechanical separation of the crystals of one enantiomer from

the other in racemic mixture based on difference in their shapes. Crystal of
the two forms have different shapes separated by magnifying lens and
forceps.

• In the crystallization process, the enantiomers crystallize separately and

form two macroscopically different kinds of crystals with a mirror-image
relationship. These crystals can be separated manually with a pair of
tweezers.

• Drawbacks: This methods is time consuming and every compound can not
be crystallized at room temperature. 71
There are two primary methods of crystallization for enantiomeric resolution.

[A]. Preferential crystallization: This method involve seeding of a saturated

solution of the racemic mixture with a pure crystal of one of the two
enantiomers. The soluition now become supersaturated with respect to the
added enantiomers. It begins to crystallize out. This process requires no
resolving agent.

[B]. Diastereoisomeric crystallization (most attractive method):

Derivatization of racemic compounds is possible with resolving agent
(optically pure reagents) forming pairs of diastereoisomers (e.g. salt
formation between an amine and a carboxilic acid) which can be separated by
conventional techniques in chemistry and finally simple deprotonation affords
the pure enantiomer.

Note: Diastereoisomeric crystallization has been the dominant technique

among industrial pharmaceutical companies for the resolution of ibuprofen
enantiomers. This method is often referred to as classical resolution.
72
[5]. Kinetic Resolution of Enantiomers:
• This method is based on the fact that one of the enantiomer of racemic mixture
reacts faster than other with the resolving agent (optically active enantiopure
compound).
• Treatment of a racemic mixture with a limited amount of a chiral reagent will
convert one of the enantiomers to product in preference to the other. Since this is
based on different reaction rates, the separation technique is called kinetic
resolution.
• If the difference is large enough, the enantiomers can be separated by
stereoselectively converting only one of the enantiomers, while the desired
enantiomer remains. After workup one enantiomer will be recovered unchanged
while the other will have been converted to a new different chiral product.

• Example: Menthol reacts faster with (+) mandelic acid than with (-) mandelic acid.
Thus with difference in kinetics of reaction, racemic mixture can be seperated.

Important Condition: The efficiency of the kinetic resolution will depend on the
relative rates of reaction of the two enantiomers. If rates of reaction (selectivity
factor) vary by > 100, then the recovered enantiomer will be >99% optically pure.
Lower selectivity factors will lead to less pure enantiomers.
73
After separation,
74
[6]. Precipitation: This method is based on formation of precipitate by reaction
between any reagent and racemic mixture. Example: (+) narcotine & (-) narcotine
when dissolved in HCL, precipitates (+) narcotine.

• (Narcotine an alkaloid present in opium; used as a nonaddictive antitussive.)

Other Resolution Methods:

• Gas chromatography-mass spectrometry (GCMS), electrochromatography,
capillary electrophoresis and nuclear magnetic resonance (NMR) have also been
utilized as potential analytical techniques in enantiomeric separation of ibuprofen.
These methods have proven to be less useful due to their inability to achieve
baseline resolutions or their inability to remove the free acid of ibuprofen after
separation.
• A recent development in the separation of ibuprofen enantiomers has been in
supercritical fluid chromatography. The most commonly used supercritical fluid is
carbon dioxide, which has chemical inertness and low toxicity.

• Supercritical fluid chromatography (SFC) behaves in a way similar to normal phase

high pressure liquid chromatography, but can be run three to ten times faster than
normal phase HPLC. 75
 Stereochemical Descriptors
Descriptor: “A descriptor is in chemical nomenclature a prefix placed before
the systematic substance name, which describes the configuration or the
stereochemistry of the molecule.”

Types of Stereochemical Descriptors:

• In stereochemistry, following types of descriptors are usually used:

1. (R)/(S) Notation (As per Cahn-Ingold-Prelog (CIP) Sequence Rules).

2. E and Z System.
3. Cis and Trans System (Already discussed).
4. D and L System.
5. Erythro and Threo System.

• Note: Notation means a hint or sign.

76
[1]. (R)/(S) Notation (As Per Cahn-Ingold-Prelog (CIP) Sequence Rules):
• For tetracoordinate carbon and related structures we use the Cahn–
Ingold–Prelog system. Cahn, Ingold and Prelog introduced this systematic
notation during the period 1951-1956.

• This notation allows us to define in a clear manner the absolute

“configuration of a drawn stereogenic centre” by assigning it as either (R)
or (S).

• In order to use this notation the first thing to do is to assign an “order of

priority to the atoms of the groups” directly attached to a stereogenic
centre.

• In order to make this easy to remember, a set of rules for specifying the
configuration about a stereocenter are used.

• In this system highest priority group is given number 1, whereas the

lowest priority group is given number 4. 77
Priority Rules:
Rule 1: Each atom bonded to the chiral center is assigned a priority based on atomic
number; the higher the atomic number, the higher the priority. Lone pairs of
electrons are assigned the lowest priority.

Rule 2: Molecules where two or more of the atoms directly attached to the
stereogenic centre are the same, look to the next set of atoms; priority is assigned at
the first point of difference.

Rule 3: If two atoms bonded to the stereogenic center under comparison are
isotopes, the one with higher mass is assigned the higher priority. Example: In
comparing the three isotopes of hydrogen, the order of priorities is:
78
R,S Priorities of Some Common Groups

79
80
Rule 4: Atoms participating in a double or triple bond are considered to be
bonded to an equivalent number of similar atoms by single bonds.

Rule 5: Having established the priorities, we now view the molecule so

that the atom/group with lowset priority is pointing away from us in space.
Finally, we count around the face of the molecule which is pointing
towards us the three other groups in order of decreasing priority.
If moving from the highest (#1), to the second (#2), to the third (#3) priority
ligand involves a clockwise direction, the center is termed R (for "Rectus" →
Latin= "right").
81
• An anti-clockwise decreasing order defines an (S)-configuration (S for
"Sinister" → Latin= "left"). The R or S is then added as a prefix, in
parenthesis, to the name of the enantiomer of interest.

Figure: Group 1 is highest priority, group 4 is lowest priority

Example No.1: In (+)-glyceraldehyde the order of priority of the groups

is OH > CHO > CH2OH > H and the configuration is (R).

82
 Example No.2: Similarly for (-)-serine the order of priority of the groups
is NH2 > CO2H > CH2OH > H and the configuration is (S).

Example No.3:

83
[2]. E and Z System: For olefins (alkenes) and related structures we use the same
priority rules, but we divide the double bond in half and compare the two sides.

• For each carbon of an olefin, assign one ligand high priority and one low
priority according to the same priority rules.

• If the two high priority ligands lie on the same side of the double bond, the
system is Z (zusammen); if they are on opposite sides, the system is E
(entgegen).

[3]. Cis and Trans System (Already Discusses): If a H-atom is on each carbon of the
double bond, however, we can also use the traditional ‘‘cis’’ and ‘‘trans’’
84
descriptors.
[4]. D and L Notations: In organic chemistry D and L notations are used
specifically to describe the absolute configurations of sugars and amino acids.

• In sugars, the position of the hydroxyl group at second last carbon determines
whether it is D sugar or L sugar.

• If the hydroxyl group is on the right side on that carbon then it is called D-
sugar and if it is on the left side, then it is named L-sugars.

Example: Glyceraldehyde has been chosen as arbitrary standard for the D and L
notation in sugar chemistry. Because, this has an asymmetric carbon and can
exist as a pair of enantiomers. D- and L-glyceraldehyde shown in Fischer
projection form are as follows:

85
• In amino acids only, glycine is achiral and remaining all amino acids are
chiral, and their configuration is determined by the location of amino group
(-NH2) on alpha carbon of amino acid.

• If the amino group (-NH2) is on right side, it is called D- amino acid and if the
amino group (-NH2) is on left side then it is called L-amino acid.

• All the chiral amino acids obtained from proteins have L configuration.
86
Important Considerations:
1. Most natural sugars are D- and most natural amino acids are L- .

2. The D and L descriptors derive from only one stereogenic center in the
molecule and are used to name the entire molecule.

3. In contrast, normally a separate R/S or E/Z descriptor is used to name each

individual stereogenic unit in a molecule.

4. d- and l- is the exact same with (+) and (-) notation. While (+) and (-)
notation corresponds to the optical activity of the substance, whether it
rotates the plane of polarized light clockwise (+) or counterclockwise (-).
87
 How is d/l isomerism different from D/L isomerism?

• Answer: d or l system is regarding optical isomerism and gives information

about how the molecule rotates the plane polarized light.

• d - dextro (right) and l - leavo (left). d and l are used to represents

dextrorotatory and levorotatory compounds respectively in organic chemistry.

• Capital “D” and “L” notations has nothing to do with optical isomerism (d/l).

• D or L system is configuration of a molecule with respect to Glyceraldehyde.

When a molecule is written according to fischer configuration, if 2nd carbon
from bottom has -OH group on right hand side its called D. If it is on the left its
called L.

• And remember bottom most should be CH2OH and 2nd from bottom should
have H and OH.
88
• D and L do not indicate whether the compound rotates polarized light to the
right or to the left.

• For example, D-glyceraldehyde is dextrorotatory, whereas D-lactic acid is

levorotatory.

• In other words, optical rotation, like melting or boiling points, is a physical

property of a compound, whereas “R, S, D, and L” are conventions humans
use to indicate the configuration of a molecule.

89
90
[5]. Erythro and Threo: If the two stereogenic centers have two groups in
common, we can assign the terms erythro and threo.

• To determine the use of the erythro and threo descriptors, draw the
compound in a Fischer projection with the distinguishing groups on the top
and bottom.

• If the groups that are the same are both on the right or left side, the
compound is called erythro; if they are on opposite sides, the compound is
called threo.

• The erythro/threo system distinguishes diastereomers. See the examples

given below.

91
92