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Isomers
1
Structural Isomers

Structural isomers have the same
molecular formulas but they differ in
their structural formulas.
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Structural Isomers
C4H10O
 C6H14
 C7H16
 C6H12

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Stereoisomers


Stereo isomers have the same
structural formulas but they differ in
their spatial arrangements.
There are two types of
stereoisomerism
1.
2.
Conformational isomerism
Configurational isomerism
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1. Conformational isomers
-
Single bond rotation, rotate freely
Higher energy
(eclipsed)
Lower energy
(staggered)
2. Configurational Isomers
Interconverted only by the breaking of
bonds
 There are 2 types of configurational
isomers
A. Geometric (cis/trans, E/Z)
B. Optical isomers

A. Geometrical isomers



Geometrical isomers occur in organic
molecules where rotation around a bond
is restricted
This occurs most often around C=C
The most common cases are around
asymmetric non-cyclic alkenes
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Geometrical isomers



Carbon to carbon double bonds are made up of a s and a
p bond.
The p bond is formed from the combination of two p
orbitals, one from each of the two carbon atoms
The two p orbitals must be in the same plane to combine
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Geometric Isomers in alkenes
2 substituents
cis/trans system

A cis isomer is one in which the substituents
are on the same side of the C=C
•

cis – 2 – butene
A trans isomer is one in which the substituents
are on the opposite sides of the C=C
trans – 2 – butene
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Geometric Isomers in alkenes
3 or 4 substituents
E/Z system
CIP system ranks according to atomic number,
higher atomic number outranks lower atomic
number.
E : higher ranked substituents on opposite sides
Z : higher ranked substituents on same side
Geometric Isomers in alkenes
3 or 4 substituents
E/Z system
Br > F
Cl > H
higher Br
C
lower
F
Cl
higher
H
lower
C
Zusamen – together (German)
(Z )-1-Bromo-2-chloro-1-fluoroethene
Geometric Isomers in alkenes
3 or 4 substituents
E/Z system
Br > F
lower
Cl > H
F
C
higher Br
Cl
higher
H
lower
C
Etgegen – opposite (German)
(E)-1-Bromo-2-chloro-1-fluoroethene
Geometric Isomers in alkenes
3 or 4 substituents
E/Z systemles
When two atoms are identical, compare the
atoms attached to them on the basis of their
atomic numbers. Precedence is established
at the first point of difference.
—CH2CH3
—C(C,H,H)
outranks
—CH3
—C(H,H,H)
Geometric Isomers in alkenes
3 or 4 substituents
E/Z system
Evaluate substituents one by one.
Don't add atomic numbers within groups.
—CH2OH outranks —C(CH3)3
—C(O,H,H)
—C(C,C,C)
Geometric Isomers in
Cycloalkanes

Ring structures like C=C restrict
rotation and therefore can result in cis
and trans isomers
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Properties of Geometrical
Isomers
The chemical properties of geometrical isomers tend
to be similar but their physical properties are different
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Properties of Geometrical
Isomers
The trans isomer has a
much higher melting point.
Unlike the cis isomer there
is little intra-molecular
hydrogen bonding
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B. Optical Isomers


Optical isomerism is present in all
compounds that contain at least one
asymmetric (chiral) carbon atom
An asymmetric carbon atom has four
different atoms or groups attached
In this case there are
two different ways to
arrange the four groups
around the chiral
carbon atom (shown in
red)
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Optical Isomers
While these structures may
look identical, in three
dimensions they are mirror
images of each other. Such
molecules are called
enantiomers.
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Distinguishing Enantiomers
Optical isomers can be distinguished by the way
they interact with plane polarized light
Polarized light
Polarized light is light that has been passed through a
polarizing prism or filter. As a result the light vibrates in a
single plane.
Distinguishing Enantiomers
Optical isomers can be distinguished by the way they
interact with plane polarized light. One enantiomer will
rotate polarized light to the right, the other to the left.
Racemic mixture equal amounts of both enantiomers does
not alter light
Properties of Optical Isomers


Apart from their optical activity enantiomers generally
have similar physical and chemical properties.
The chemical properties may be significantly different
when the enantiomers interact with other optically
active compounds.
Optical isomer
limonene
(+) isomer strong smell of oranges/lemons
(-) isomer strong smell of pine
needles/peppermint
Optical isomer
Thalidomide
(+) isomer is a sedative
(-) isomer is a teratogen
B.10 Stereochemistry in
Biomolecules
Stereochemistry of biological molecules
1) 2-amino acids
2) Carbohydrate
3) Fatty acids
4) Retinoids
1) 2 – amino acids
-
-
All amino acids have a chiral centre
except glycine.
All amino acid enantiomers are Lisomers
wedge-dash
fischer projections
2-amino acids
Fischer projections are drawn as a cross with
the carbon chain vertically, so at the top is
COOH (amino acids) or C=O (carbohydrates)
amino acids
carbohydrates
2-amino acids
L – enantiomers have amino group on the left
D – enantiomers have amino group on the right
2-amino acids
- Other
method for identifying enantiomers is called
the CORN rule (COOH, R and NH2)
- Position molecule so H atom at C-2 faces away
- CO – R – N is spelled clockwise you have D –
enantiomer
- CO – R – N is spelled anti-clockwise it is L –
enantiomer
2-amino acids
2) Carbohydrates
- For the D and L system the C=O is at the top and
you look on which side the OH is on the chiral carbon
furthest from the C=O.
2) Carbohydrates
Enantiomers – mirror images
Diastereomers – when 2 stereoisomers of a
compound have different configurations at one or
more (but not all) chiral centres
Epimers – when 2 diastereomers differ at only 1
chiral centre.
2) Carbohydrates
cyclic monosaccharides
 -  system
Each monosaccharide can produce 2 cyclic forms
that differ in the orientation of the –OH group at C-1
atom in glucose (aldoses = aldehyde)
2) Carbohydrates
cyclic monosaccharides
 -  system
or C-2 atom in fructose (ketoses = ketone)
2) Carbohydrates
cyclic monosaccharides
 -  system
-
 tend to be more water soluble
The conversion b/n  and  occurs
through open chain isomer
2) Carbohydrates
Cellulose
 -  system
-
-
Cellulose is a polymer of -glucose,
most abundant polysaccharides in
plants.
Glucose residues are joined by -1,4glycosidic links
2) Carbohydrates
Cellulose
 -  system
-
-
-
Starch and glycogen are polymers of
-glucose and are branched polymers
No branching in cellulose causes
stronger intermolecular forces (Hbonds) causing insolubility in water,
stronger and lower dietary value
Humans and animals cannot digest
cellulose. Ruminants contain bacteria
that produce cellulase in their
digestive system
2) Carbohydrates
Cellulose
 -  system
-
Common name is dietary fibre, can’t
be digested but
-
-
-
Cleans and prevents constipation
Reduces appetite
Helps prevent obesity
Regulates absorption of sugars and
bile
Reducing diabetes and cholesterol
3) Fatty acids and
triglycerides
 -  system
-
-
-
- naturally occuring fatty acids have
cis C=C, so not linear, weaker
intermolecular forces, therefore cisfats liquids at room temperature
Hydrogenation (similar to addition of
alkenes) turns cis-fats into saturated
fats. Requires high temp. and nickel
catalyst.
High temp. of process leads to some
cis-fats becoming trans-fats
3) Fatty acids and
triglycerides
 -  system
-
High temp. of process leads to some
cis-fats becoming trans-fats
-
Melting points are higher than cis-fats
and lower than saturated fats of equal
length.
3) Fatty acids and
triglycerides
 -  system
-
-
-
-
Trans-fats trace amounts present
naturally occuring.
15% in margarine (man-made)
High in fast food industry
High consumption leads to high LDL
increases risk of heart disease
Difficult to metabolize stored in fat
increased obesity
Links to diabetes and Alzheimer’s
4) Retinoids
Vitamin A
-
-
Vitamin A refers to a group of
polyunsaturated compounds, one of
which, retinal (a long chain aldehyde)
is involved in vision chemistry.
In the photoreceptor cells 2
stereoisomers for retinal (cis-retinal
and trans-retinal) which can be
converted into each other with visible
light or enzymes
4) Retinoids
Vitamin A
-
-
-
-
Opsin is a protein that can reversibly bind cisretinal
Rhodopsin is the opsin/cis-retinal combination,
which is a light sensitive pigment.
CN extends electron conjugation and allows it
absorb visible light in the blue and green regions so
rhodopsin looks purple in colour
Other opsins produce cis-retinal complexes with
different absorption spectra (colour vision)
4) Retinoids
Vitamin A
-
-
-
Whe rhodopsin absorbs a photon of visible light,
the residue of cis-retinal turns into trans-retinal
and the protein conformation changes.
This triggers a cell response that sends
electrical signal to nervous system.
Trans-retinal detaches from opsin goes through
visual cycle and converts back to cis-retinal and
recombines with opsin to reform rhodopsin