CHAPTER-2

Stereochemistry, conformation and

stereoselectivity
 Chapter Contents
• Introduction
• Configuration and conformation
• Optical isomerism and optical activity
• Chiral/achiral and symmetry/asymmetry concepts
• Properties of enantiomers and diastereoisomers
• R/S and D/L notation for stereoisomers
• Fischer projection
• Syn/Anti and Cis/Trans isomerism
• Meso compounds
• Racemization and resolution of racemic mixtures
• Asymmetric synthesis
 Introduction
 Definition of stereochemistry
• Is the arrangements of atoms of a molecule in three-
dimensional space
• Molecules that have identical connectivity and atom constitutes
but differ in 3D-structure are called stereoisomers
• The difference in arrangement between molcules at one or more
atoms is called configuration
• The various shapes that molecules have by single-bond rotations
without bond breaking is known as conformation
• The stereochemical nature of molecules both in terms of
configuration and conformation impacts their reactivity
 Configuration at double bonds
Naming of stereoisomers: Based on Cahn-Ingold-Prelog priority
rules-in order of decreasing atomic number

• The higher-priority groups at each carbon on the same side

of the double bond is called the Z-isomer (for together)
• .The isomer with the higher-priority substituents on opposite
sides is called the E-isomer (for opposite)

Example
 Configuration at cyclic compounds

Similar to the double bond, substituents can be on the same (cis) or

opposite (trans) side in cyclic compounds

wedged Dashed bond

bond

Stereoisomers also arise when two rings share a common bond

 Configuration at tetrahedral atoms/single bonds

• Carbon atoms with all four substituents are different have tetra
hedral geometry with sp3 hybridization
• Such atoms can be arranged in two different ways. The two
different arrangements are mirror images of one another, but they
cannot be superimposed.

• Molecules with four nonidentical substituents and

nonsuperimposable are called chiral
• The central carbon atom is called stereogenic center or stereocenter.
• They have two configurations, clockwise direction assigned as R
(for rectus) and anticlockwise direction assigned as S (for sinistre)
 Atoms are arranged in decreasing priority,
1>2>3>4. The molecule is then viewed opposite
from the lowest-priority group, that is, the
group is placed behind the stereocenter and
away from the viewer

Examples

 The two nonsuperimposable mirror image molecules are called

an enantiomeric pair and each is the enantiomer of the other
 Property and optical activity of enantiomers
 Under achiral environment
• Enantiomeric compounds have identical property
• They have same solubility, physical and spectroscopic properites
• And they show same chemical reactivity toward achiral reagents
 Under chiral environment
• They have different properties. They react at different rates toward
chiral reagents and respond differential to chiral catalysts
• Biologically, enantiomers show different physicological
responses as biological receptors are chiral.

For instance, the odor of the R-

(spearmint oil) and S- (caraway seed oil)
enantiomers of carvone are totally
different
 Optical activity/rotation
• The ability or property of compounds to rotate the plane
polarized light is called optical activity.
• The magnitued of rotation is measured by polarimeter instruments.
• Enantiomers also rotate the plane polarized light differently.
• They rotate the light in equal amount, but opposite direction.

• Compounds have two types of rotations

- Observed rotaion (α)- which depends on the conditions of
measurements i.e. concentration, path length, solvent and wavelength of
the light.
- Specific rotation-which is characteristic of indivitual enantiomer and
designated by [α]589, the subscript is a wave length.

Observed
rotation
where, c is the concentration in g/100 mL and l is the
path length in decimeters.
 • A chiral compound can be a pure entantiomer or mixture of
both enantiomers
• Enantiomerically pure compounds are called homochirals or
enantiopures.
• If a cmpound contains a 1:1 mixture of enantiomers it will
have a net zero optical rotation because rotations of the two
enantiomers will cancle each other.
• Compounds with 1:1 mixture of enantionmers are called
racemic mixture or racemate.
• Racemic mixture has different propreties including melting
point and solubility in solid state from the indivitual pure
enantiomers.
 The composition of a mixture of enantiomers other than 1:1 is expressed by the
enantiomeric excess (e.e) which is the percentage excess of the major enantiomer
over the minor enantiomer and calculated by:
Or
 • Optical purity: It indciates the observed rotation of the mixture
retative to the pure enantiomer.
• This observed rotation is the product of (% Major −% Minor) ×
[α]λ since the rotation of the two enantiomers cancel each other out
• If [α]λ is known, measurement of α allows the optical purity and
enantiomeric excess to be determined by:

• e.e. can also be measured by NMR spectroscopy,

chromatography, and capillary electrophoresis
• Measurement of rotation in terms of wavelength is also used to
determine the configuration of a chiral molecule and then to study
structure of compounds. This technique is called optical rotatory
dispersion (ORD)
 Molecules with multiple stereogenic centers

 Molecules can have more than one stereogenic centers, including

double bonds with Z or E configurations and asymmetrically
substituted tetrahedral atoms.
 The maximum number of stereoisomers that can be generated
from n stereogenic centers is 2n.
 Such molecules can be represented in an extended conformation
with the longest chain aligned horizontally.
 The configuration of each center is specified as R or S, or
characterized as syn or anti using wedged and dashed bonds.
Example: 2,3,4-trihydroxybutanal Opposite configuration at
each center

Opposite configuration at
each centre

 Molecules that are stereoisomeric but are not enantiomeric are

called diastereomers
 Diastereomeric molecules have the same constitution (connectivity)
but differ in configuration at one or more of the stereogenic centers
 The positions in two diastereomers that have different
configurations are called epimeric. For exmple, anti-2R,3R and
syn-2R,3S stereoisomers have the same configuration at C(2), but
• Fischer projection formulas-another representation of chiral
molecules
• The main chain of the molecule is aligned vertically, with the most
oxidized end of the chain at the top.
• The chirality of the highest-numbered chiral center (the one most
distant from the oxidized terminus or the one closest to the
bottom), is specified as D (to the right) or L (to the left)
• This designation is based on the D- or L-enantiomer of
glyceraldehyde, which is the reference compound.

Most oxidized end

Highest numbered chiral

center
 The relative configuration of adjacent substituents in a Fischer
projection formula are designated erythro if they are on the same
side and threo if they are on the opposite side.
Fischer projeciton represents
an eclipesed conformation of
carbon chains. Due to this
Fischer representation opposite
to extended staggered
representation.

Newman projection

Extended
Fischer staggered
projection representation
 Relationship between chirality and symmetry
 Molecules that possess certain elements of symmetry are not
chiral, because the element of symmetry ensures that the
mirror image forms are superimposable.
 Plane of symmetry is good example which divides a molecule
into two halves that have identical placement of substituents on
both sides of the plane

Typical example is 2-propanol- a tetrahedral molecule with

two idnetical subsittuents. The plane subdivides the 2-H
and 2-OH groups and the two
methyl groups are identical.
The chemistry of tartaric acid (2,3-dihydroxybutanedioic
acid)
 Tartaric acid has three stereoisomers- two chiral and one achiral
 In the achiral stereoisomer, the substituents are located with respect to each
other in such a way as to generate a plane of symmetry. This achiral
stereoisomer is called meso tartaric acid.
 Compounds that contain two or more stereogenic centers but have a plane
of symmetry are called meso compounds.
 Meso compounds are achiral and do not rotate plane polarized light.
 Configuration at prochiral centers

 Prochiral centers have two identical ligands, such as two

hydrogens, and are achiral.
 However, these identical ligands are topologically nonequivalent
or heterotopic and the remaining two substituents are different.
 If either of the identical groups is replaced by a different ligand, a
stereogenic center is created. The two positions are called
enantiotopic
Prochiral Prochiral center
center
Pro-R or Pro-S
Propane-1,3-diol-example of
prochiral molecule.
 • Unsymmetrically substituted carbonyl groups are another
prochiral centers
• The carbonyl group is said to have an re face and an si face.
• Achiral reagents can not distiniguish these two faces. However,
chiral reagents can do and provide unequal amnounts of
enantiomers.

• Carbon-carbon double bonds,

present two prochiral faces.

Maleic acid fumaric acid (Z) gives meso or achiral

(E) compounds

E- and Z-butenedioic acid subjected to syn-dihydroxylation

 Reaction of enantiotopic molecules with biological enzymes
 Biological reactions involve chiral enzymes. Therefore,
enantiotopic groups, diastereotopic groups and faces typically show
different reactivity.

reduction from the re face

The oxidizing enzyme called alcohol
dehydrogenases, selectively remove the
pro-R hydrogen.

hydroxylation

Fumaric acid
L-malic acid (S-2-hydroxybutanedioic
acid)
hydroxylation of fumaric acid via Fumarase enzyme
 Separation/resolution of enantiomers by chemical method

• Most naturally occurring chiral compounds exist in enantiomerically

pure form
• Because all living organisms involve reactions of enantiomerically
pure materials like carbohydrates, proteins, and DNA
• However, man made compounds are mostyl racemic mixtures since
racemic and/or achiral reactants, reagents, catalysts, and solvents are
used
• But, man made chemical reactions can also provide enantiopure
compounds if chiral starting materials, reagents, catalysts or solvents
are used
• But, man made chemical reactions can also provide enantiopure
compounds if chiral starting materials, reagents, catalysts or
solvents are used.
• The process of separating a racemic mixture into its
enantiomers is called resolution.
• Racemic mixtures can be separated into the two enantiomeric
forms using enantiomerically pure compound, often a naturally
occuring material, as a resolving agent.

pure enantiomer

R-A-S-B & S-A-S-B are

diastereomeric products
 Resolution of 3-methyl-2-phenylbutanoic acid
R S

Also, enantionmers can be resolved based on the difference in rates of reaction

with a chiral reagent. The rates of reaction of each enantiomer with a single
enantiomer of a chiral reagent are different because the transition structures and
intermediates (R-substrate…R-reagent) and (S-substrate R-reagent) are
diastereomeric. Kinetic resolution is the term used to describe the separation of
enantiomers on the basis of differential reaction rates with an enantiomerically
 Conformation
 Configuration is the geometric arrangement fixed by the chemical
bonds within the molecule
 Conformation is a molecular structure in which a molecule can attain
different shapes without breaking any covalent bonds
 They differ from one another as the result of rotation at one or more
single bond
 Conformational analysis is the process of relating conformation to the
properties and reactivity of molecules
 For example, The energy barrier for rotation of carbon-carbon single
bonds is normally small, less than 5 kcal/mol
 Conformation of acyclic compounds
- Ethane-a good example to show the conforamtion of acyclic compounds.
- The two methyl groups in ethane can rotate with respect to one another
-There are two unique conformations, called staggered and eclipsed.
-The barrier to rotation is called the torsional barrier
- van derWaals repulsions are a major factor in conformational preferences and energy
barriers but not for ethane since hydrogens do not come close enough to account for the
barrier to rotation
- The barrier becomes significantly larger only when additional steric components are
added

Eclipsed-maximum energy

Staggered-minimum energy

-The difference between the two is 2.88 kcal/mol.

-The rate of rotation is about 6×109 s−1 at 25 oC which is fast
Conformation of simple alkenes-The case of propene

-There are two families of conformations available to terminal alkenes: eclipsed and
bisected conformations
- To correlate the rotational barrier of propene to ethane, consider the double bond as a
“banana bond”
Consider as banana bond

Propene
related to staggered ethane
related to elipsed ethane

Increasing the size of the group at C(3)

increases the preference for the eclipsed
conformation
Eclipsed 1,3-allylic strain
C(3)
Other compounds having eclipsed stable conformation
Eclipsed Eclipsed Eclipsed

Preffered conformaiton for ethanal, propanal and 3,3-dimethyl

butanal

steric strain
Ketones eclipsed conformation

van der Waals repulsion between the

hydrogens on C(1) and C(4)
stable conformaiton

Axial equatorial-stable-preffered
due to no H-CH3 axial-axial
interaction
 Stereoselective and stereospecific reactions

 It deals with the reactivity and stereochemistry of organi compounds

 Many reactions can provide two or more stereoisomeric products. If
a reaction shows a preference for one of the stereoisomers, it is
called stereoselective.
 Stereoselectivity is closely related to the mechanism of the reaction.
 Reactions in which stereoisomeric reactants each provide
stereoisomeric products are called stereospecific.
Examples of stereoselective reactions

A) Catalytic hydrogenation- Unfunctionalized alkene usually reacts by

preferential syn delivery of hydrogen from the less hindered face of the double
bond.
- Hydrogenation can be carried out using either finely dispersed metal
(heterogeneous, Pt, Pd) or soluble (homogeneous) metal complexes

Mechanism
Pi-complex

Adsorbtion
B) Hydride reduction of cyclic ketones-Unhindered cyclohexanones normally
react with NaBH4 and LiAlH4 by preferential reagent approach from the axial
direction forming mainly the equatorial alcohol.
axial direction

equatorial alcohol

Bicyclic ketones are generally reduced by hydride approach from the less
hindered face of the carbonyl group
 C) Stereoselective nucleophilic additions to acyclic carbonyl groups

• The stereochemistry of nucleophilic addition to acyclic aldehydes and ketones

is influenced by near by substituents
• When there is a stereogenic center adjacent to the carbonyl group, two
diastereomers can be formed, depending on the direction of the approach of the
nucleophile.

Crahm’s rule: the largest α group was eclipsed with the other carbonyl substituent

Felkin-Ahn model: the largest substituent will be placed perpendicular to

the carbonyl group. The major product results from the nucleophile
approaching opposite to the largest substituent.
Examples of stereoselective
nucleophilic addition

Examples of stereospecific reactions

• In stereospecific reactions the configuration of the product is
directly related to the configuration of the reactant and is
determined by the reaction mechanism.
• Stereoisomeric reactants give different, usually stereoisomeric,
products.
• The reaction mechanism determines the stereochemical
relationship between the reactants and products
• stereospeceficity may be lost or altered if there is a change in the
mechanism
For example: A) SN2 vs SN1
reaction

the mechanism shifts to SN 1

because of a change in reactants
B) syn and anti addition to double bonds or reaction conditions,
stereospecificity is lost.

Example:

Exceptional-if carbocation is
Bromination of alkene first formed
 Other types of stereospecific reactions
Alkene Dihydroxylation by OsO4-Catalysis and Epoxide Ring Opening

Hydroboration:
 Analysis and separation of enantiomeric mixtures
Different techniques can be used for determination of the enantiomeric purity of a
chiral compound. The amount of rotation can provide this information if the
specific rotation [α] is known. However, polarimeter is not very sensitive,
especially if the specific rotation is relatively low

Chiral shift reagents and chiral solvating agents: Very common in Organic
Chemistry using NMR spectroscopy with chiral shift reagents, which are
complexes of a lanthanide metal and a chiral ligand

Chiral solvating agents

Pirkle alcohol: trifluoroethanol group, which provides a

chiral shift reagents strong hydrogen bond acceptor, and the anthracene ring,
which generates anisotropic shielding.
 Separation of enantiomers based on physical technique
i) Separation by chromatography:
-It is based on use of a chiral stationary phase (CSP).
-Chromatographic separations result from differential interactions of the
enantiomers with the solid column packing material. The differential
adsorption arises from the diastereomeric nature of the interaction between the
enantiomers and the CSP. Hydrogen bonding and aromatic interactions often
contribute to the binding.

Example of chiral packing material-polysaccharides and amino acid derivatives

ii) Resolution by Capillary Electrophoresis

- The principle of electrophoretic separation is differential migration of a charged

molecule in a polymer matrix under the influence of an electric field.
- Gel electrophoresis, a very important bioanalytical technique, is done in a
polyacrylamide gel and depends on molecular size and charge differences to achieve
differential migration. It is primarily applied to macromolecules, such as polypeptides
and oligonucleotides.
- Capillary electrophoresis (CE) has been developed as a technique for analysis of
small chiral molecules, especially drugs.
- Cyclodextrins, which are cyclic oligosaccharides, are among the chiral selectors
- Macrocyclic antibiotics such as vancomycin and rifamycin B are also used a chiral
selectors.
 Cyclodextrins

All the enantiomeric separations based on chiral molecules depends upon a

combination of intermolecular forces, including electrostatic attractions,
hydrogen bonding, and stacking
 iii) Enzymatic resolution and desymmetrization

• Enzymatic resolution is based on the ability of enzymes (catalytic

proteins) to distinguish between R- and S-enantiomers or between
enantiotopic pro-R and pro-S groups in prochiral compounds
• The selective conversion of pro-R and pro-S groups is often
called desymmetrization or asymmetrization
• The criterion for a successful enzymatic resolution is that one
enantiomer be a preferred substrate for the enzyme
• the enantioselectivity is quite high, since enzyme-catalyzed
reactions typically involve a specific fit of the reactant (substrate)
into the catalytically active site
• The limitation of this method is that the compound to be resolved
must be an acceptable substrate for the enzyme
• If not, there will be no reaction with either enantiomer
 Examples of versatile enzymes

1) Esterases and lipases: catalyze formation or hydrolysis of esters.

pig liver esterase (PLE) and porcine pancreatic lipase are the most
commonly used of the hydrolytic enzymes
2) Proteases and acylases or amidases: catalyze amide formation and
hydrolysis
3) Epoxide hydrolases: which open epoxide rings
4) oxido-reductases: which interconvert alcohols and carbonyl
compound by oxidation and reduction.