U1 Isomerism 2017
U1 Isomerism 2017
Of
natural products
1
Course objectives
• Introduction
• Stereochemistry
• Isomerism
• Enantiomers, diastreomers and meso cpds
• Significance of stereoisomerism
3
Introduction
Chemistry:
• Is a science that deals with the
composition and properties of
substances and various elementary
forms of matter.
• Chemistry is the science of the
composition, structure, properties
and reactions of matter, especially of
atomic and molecular systems.
4
Cont…
Pharmacy:
• Is a branch of the health sciences
dealing with the
• preparation,
• dispensing,
• proper utilization of drugs.
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Natural products
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Con…
• Natural products
• Are products are made by enzymes from various natural
sources, plants, microbes and animals.
• Natural products can be
• An entire organism, A part of an organism, An extract,
Pure compounds
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1.1. Isomerism
• Isomerism (Greek isos, equal; meros, parts) is the
occurrence of two or more compounds that have the same
molecular formula but different physical, chemical and
biological characteristic due to structures and appearance
in space.
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Isomerism cont.
• There are two main classes of isomerism
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10
Cont…
CHAIN
ISOMERISM
b)
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Chain/skeletal/: different arrangements of the carbon
skeleton, similar number of atoms and functional groups with
the same. chemical properties, slightly different physical
properties, more branching = lower boiling point
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Positional: Different positions of side
chains, substituents, functional groups,
double bonds, triple bonds, etc. on the
parent chain
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Functional Group: The existence of various
functional groups causes functional
isomerism. The functional isomers have the
same molecular formula but possess
different functional groups.
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4. Metamerism: When various alkyl groups are
joined to the same functional group, metamerism
results. For example, the ether functional group is
present in the following metamers. However, the type of
alkyl groups that are joined to the oxygen atom in each
one makes a difference.
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5. Tautomerism- The dynamic equilibrium between two
compounds having the same chemical formula is
referred to as tautomerism. The tautomers live in
dynamic equilibrium and have several functional groups.
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6 Ring chain isomerism- Ring chain
isomers are substances with the same
chemical formula but an open chain and
cyclic structure. Ring chain isomers
include propene and cyclopropane, for
instance.
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1.1.2 Stereoisomerism
• Stereochemistry is a science, in organic
chemistry, which deals with the chemistry
of molecules in three dimensions
(Greek: stereos, solid).
• A clear understanding of stereochemistry
is crucial for the study of complex
molecules that are biologically important,
e.g. proteins, carbohydrates and
nucleic acids, and also drug molecules,
especially in relation to their behavior and
pharmacological actions.
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Stereochemistry
• Stereochemistry is the study of the static
and dynamic aspects of the three-
dimensional shapes of molecules
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Stereoisomerism cont.
Stereoisomers
• Are compounds made up of the same atoms
connected by the same sequence of
bonds, but having different three
dimensional structures
• There are two major types of stereoisomers:
i. Conformational isomers and
ii.Configurational isomers
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HO HO
O
O HO
HO
HO
OH
HO HO
OH
OH
α-Glucose β-Glucose
OH
O OH
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1.1.2.1 Conformational isomers
• Atoms within a molecule move relative
to one another by rotation around
single bonds.
• Such rotation of covalent bonds gives
rise to different conformations of a
compound.
• Each structure is called a conformer or
conformational isomer.
• Generally, conformers rapidly
interconvert at room temperature.
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• Stereoisomers which are interconvertible simply by
rotation of one part of the molecule with respect to other
about a single bond.
• Eclipsed conformation:
• C-H bond opposite to each other(minimum distance)
• Staggered conformation:
• C-H bonds at maximum distance
H H
H re
d H ed
St
a g g e
H E clip
s H
H H H H
H H
1.1.2.2 Configurational
isomers
• The actual arrangement or orientation (in
space) of atoms/groups attached to the
chiral carbon (stereogenic centre or
stereocentre) is called the configuration
of a compound.
• Configurational isomers differ from each
other only in the arrangement of their
atoms in space, and cannot be converted
from one into another by rotations about
single bonds within the molecules.
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Configurational isomers cont.
• Configurational isomers: common
with C=C,C=N,N=N
• Geometric (cis-trans) isomers
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Configurational isomers cont.
• For example,
• Our left and right hands are mirror images of each other, and cannot
be superimposed on each
• Other chiral objects include shoes, gloves and printed pages 29
Cont…
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Configurational isomers cont.
• Many compounds that occur in living
organisms, e.g. carbohydrates and
proteins, are chiral
• The most common feature in chiral
molecules
• Is a tetrahedral (i.e. sp3-hybridized)
• Asymmetric carbon.
• Do not have a plane of symmetry.
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X X
W C Y W C Z
Z Z
Cl Cl
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Configurational isomers cont.
B. The chiral center
• A Carbon atom to which four d/t groups are
attached is a chiral center.
• The maximum number of isomers that can exist is
B) CH3 CH3
Br Br
Cl Cl H
H
C) H Br H
Br
F F
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Are the following pairs of compounds
consitutional isomers or stereoisomers?
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I. Geometrical isomers
• Exhibit by molecules having the same
stricture but differing in their configuration
due to molecular symmetry
• Geometrical isomerism is found in
alkenes and cyclic compounds.
• In alkenes, there is restricted rotation
about the double bond.
• When there are substituent groups attached to the double
bond, they can bond in different ways, resulting in
• Trans (opposite side) and cis (same
side) isomers
• These are called geometrical isomers.
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Cont…
H
G
C C
H G
Cis Trans
Trans-Isomer
(i) Substituent G is on opposite sides
on the double-bonded carbons
G
G
C C
H
H
Cis-Isomer
(ii) Substituent G is on same side on the
double-bonded carbons
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Geometrical isomers cont.
• They have different chemical and physical
properties.
• Each isomer can be converted to another
when enough energy is supplied, e.g. by
absorption of UV radiation or being heated at
around 300oC.
• The conversion occurs because the π bond
breaks when energy is absorbed, and the two
halves of the molecule can then rotate with
respect to each other before the π bond forms
again.
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Geometrical isomers cont.
How to designate Trans or Cis
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Geometrical isomers cont.
• The priority should be on the same basis as the
(R)/(S) system (i.e. on the basis of atomic
number).
If the two higher priority groups of the two C
atoms are on the same side of the double bond, it
is called the (Z)-isomer.
If the two higher priority groups of the two C
atoms are on opposite sides of the double bond, it
is called the (E)-isomer.
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II. Optical isomers -
enantiomers
• Optical isomerism is a property exhibited by any
compound which have the same structure but differ in their
configuration due to molecular asymmetry (whose mirror
images are non-superimposable) rotate plane polarized
light.
• Racimic Enantiomers:
• The Greek word enantio means ‘opposite’.
• A chiral molecule and its mirror image are called enantiomers or
an enantiomeric pair, they rotate in equal amount in opposite
direction.
• Diastereoisomer: rotate in different amount
• Meso type optically active but doesn’t rotate at all.
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Optical isomers cont.
• Are non-superimposable mirror image isomers can rotate the plane of
polarization of plane-polarized light.
W W CH3 CH3
X X H H
Z Z C2H5 C2H5
Y Y OH HO
A B (i) B (ii)
plane-polarized light-
A : Before passing through a solution of an enantiomer,
B : After passing through a solution of an enantiomer
I. Clock-wise (right) rotation or Dextrorotatory (D) (+)
II. Anti-clock-wise (left) rotation or Levorotatory (L) (−) 45
Cont…
POLARIMETER; used to analyse the effect optical isomers
have on plane polarised light:
A B
C D
E
F
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Optical isomers cont.
Asymmetric compounds rotate plane
polarized light
Magnitude of rotation depends upon:
1. The nature of the compound
2. The length of the tube usually expressed
in decimeters (dm)
3. The wavelength of the light source
employed; /λ/
4. Temperature of sample /T°/
5. Concentration of analyte
6. Concentration of solvent
48
Optical isomers cont.
The racemic mixture (racemates):
• A pair of enantiomers, each rotates the
plane-polarized light by the same amount,
but in the opposite direction.
• 50:50 mixtures of enantiomers are
called a racemic mixture.
• Racemic mixtures are optically ‘inactive’
(i.e. they cancel each other)
• The prefix () is used to specify the
racemic nature of such sample
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Cont…Significance of + vs -
(-) (+
)
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Cont…
Thalidomide
• 10,000-12,000 thalidomide
babies
• 46 affected countries
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Cont...
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Thalidomide Rises from the
ashes!
• Currently used for
• Cancer treatment
• Anti-inflammatory
• HIV patients
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Optical isomers cont.
Resolution
• A process where in enantiomers are
separated is called a Resolution.
• Convert the pair of enantiomers into a pair
of diastereomers
• Can be made by
• Chiral derivatising agents- acids, salts
• Chromatography- HPLC, GC, CC
• NMR spectroscopy: chiral shift reagents
• Enzymatic resolution
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Representation of Molecules in
Three Dimension
• 1) Flying-wedge or Wedge-dash Projection: is the
most widely used three dimensional representation of
a molecule on a two dimensional surface (paper). This
kind of representation is usually done for molecule
containing chiral center.
• In this type of representation three types of lines are used.
• A bold wedge or thick line - it represents bond projection towards
the observer or above the plane of paper.
• A continuous line or ordinary line - it represents bond in the
plane of paper.
• A dashed wedge or broken line - it represents bond projection
away from theobserver or below the plane of paper. Example:- CH4
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Cont…
2) Fischer Projections
• A 2D representation of chiral
molecules
• Vertical lines
• Represent bonds projecting behind
the plane of the paper
• Horizontal lines
• Represent bonds projecting out of
the plane of the paper
CHO CHO
CHO
H OH H OH
H C
CH2OH CH2OH
HO CH2OH
R-(+)- Glyceraldehyde
CHO CHO
CHO
HO H HO H
HO C
CH2OH CH2OH CH2OH
H
S-(+)- Glyceraldehyde
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Cont...
3) D and L system
Emil Fischer used glyceraldehyde
as a standard for the D and L
H O
system of designating
configuration. H OH
• Glyceraldehyde
CH2OH
Is an optically active molecule.
Glyceraldehyde
can exist as enantiomers, i.e. (+)
and (-) forms, but the sign does
not describe the exact
configuration
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cont...
• He arbitrarily took the (+) - glyceraldehyde enantiomer and assigned this as
D-glyceraldehyde
• The other enantiomer is the (-)-glyceraldehyde and this was assigned as L-
glyceraldehyde
H O
H O
H OH HO H
CH2OH CH2OH
(+)-D-Glyceraldehyde (-)-L-Glyceraldehyde
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cont...
• It can easily be identified that the only difference in the
structures of D and L-glyceraldehyde is the orientation of
the hydroxyl group at the chiral centre.
• D-glyceraldehyde –OH on the chiral C is on the
right
• L-glyceraldehyde –OH on the chiral C is on the
left.
• One must remember that there is no correlation between
• D and L configurations, and
• (+) and (-) rotations.
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Cont...
This D and L system is
• Common in biology/biochemistry,
especially with sugars and amino acids
(with amino acids, the –NH2 configuration is
compared with the –OH of glyceraldehyde)
• Particularly used to designate various
carbohydrate or sugar molecules, e.g. D-
glucose, L-rhamnose and L-alanine.
• The most generally useful, yet
suggested, way of specifying configuration
is the use of the prefixes R and S notation.
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Cont...
4) (R) and (S) system (Cahn–Ingold–
Prelog system)
• A system of nomenclature that can describe
the configuration of enantiomers more
precisely/ absolute configurations of chiral
compounds.
• R and S came from the Latin words rectus
and sinister, meaning right and left,
respectively.
• The following rules or steps are applied for
designating any enantiomer as R or S.
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Cont...
1. Arrange the ligands associated with an
element of chirality into order of priority.
• Priority Rules
• Higher atomic number is given higher
priority.
• Higher atomic mass is given higher priority
(for isotopes).
• When the proximate atoms of two or more of
the ligands are the same, the atomic number
of the next atom determines the priority; i.e.
• Proximal groups take priority over distal
groups
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Cont...
• Double and triple bonds are counted as if they were split into two or
three single bonds, respectively
C O
As if it
C O
were O C
N C
C N
As if it
C N were N C
1
Rotate 4 H
HO H 4 d to 1 Viewer
OH
2 CH2CH2CH3
2CH2CH2CH3
3
CH3
4 H
1 Viewer
OH
2CH2CH2CH3
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NEWMAN PROJECTION
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CH3CH2CH2CH3
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Chair and boat
cyclohexane ring
contain molecules
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How many stereogenic centers does each
molecule have?
Br
A)
Br
B)
CO2H O
H
B) N OH
H2N N
H
O O
SH
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Which group in each pair has the highest priority?
A) -CH3 or -CH2CH3
B) -I or -Br
C) -CH3Br or -CH2CH2Br
C CH H
B) C CH2 CH3
H
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Label each compound as R or S.
Cl
A)
H
H3C Br
CH2Br
B)
ClH2C
OH
H3C
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Enantiomers, Diastereomers
and Meso Cpds
Enantiomers
• Enantiomers are mirror image isomers
• Have the same connectivity and opposite
designations (eg, the enantiomer of (2R,3R-
Tartaric acid is (2S,3S)- tartaric acid) at
respective chiral centers
• Have identical physico-chemical properties
• Illustrative example, 2,-Bromo,3- chloro
butane
• There are two chiral carbons
• The chiral centers are at C-2 and C-3.
• The maximum number of possible isomers will be 2n = 22 = 4.
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Cont…
CH3
CH3
S Enantiomers R
H Br
Br H
Cl H
S H Cl R
CH3
CH3
CH3 CH3
R
Br H H Br S
Cl H S H Cl R
Enantiomers
CH3 CH3
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Cont…
CH3 CH3
S R
H Br Br H
Diastereomers
Cl H S H Cl R
CH3 CH3
CH3 CH3
R
Br H H Br S
Diastereomers
Cl H S H Cl R
CH3 CH3
Cl H
Mes
CH3
o
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Can be superimposed by 180 rotation.
o
Diastereomers and Meso compounds
cont.
All meso compounds can be considered
diastereomers, not all diastereomers are meso
compounds
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Enantiomers, Diastereomers and
Meso Cpds..
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Which of the following are meso compounds?
A) D) O
B) E)
Cl
C)
OH
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Label the stereogenic centers and draw all
stereoisomers.
A)
CH3CH2CH(Cl)CH(OH)CH2CH3
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Answer
A)
CH3CH2CH(Cl)CH(OH)CH2CH3
H H H H
OH HO Cl
Cl
H3CH2C CH2CH3
H3CH2C CH2CH3
H OH
H HO H
Cl
H Cl
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Brainstorming
• What is the need to study stereoisomerism in
Pharmacy?
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Significance of R vs S
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87
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What is the need to study stereoisomerism in Pharmacy?
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Significance of …cont.
• Currently there is a rapid increase of the sales
of chiral drugs in drug markets
• One enantiomeric form of a drug may be active, and the other may
be inactive, less active or even toxic.
• Proper nomenclature in describing the drugs themselves
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Significance of …cont.
• Most often only one form
shows correct physiological
and pharmacological action.
• For example,
• Only one enantiomer of morphine is
active as an analgesic
91
Significance of …cont.
• Most of the molecules that make up living organisms
are chiral, i.e. show stereoisomerism.
• For example, all but one of the 20 essential amino
acids are chiral.
• Thus, it is important to understand stereochemistry for
a better understanding of drug molecules, their action
and toxicity.
92
Significance of …cont.
• Two enantiomers of limonene produce two distinct
flavours:
• (-)-limonene is responsible for the flavour of lemons
and
• (+)-limonene for orange.
H
H
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Cont…
ANY QUESITIONS
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