1. Isomers 1

2. Structural Isomers
Structural isomers have the same molecular formulas but they differ in their structural formulas. 2

3. Structural Isomers
C4H10O
C6H14
C7H16
C6H12 3

4. Stereoisomers
Stereo isomers have the same structural formulas but they differ in their spatial arrangements.
There are two types of stereoisomerism
Conformational isomerism
Configurational isomerism 4

5. 1. Conformational isomers
Single bond rotation, rotate freely
Higher energy Lower energy
(eclipsed) (staggered)

6. 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

7. 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 7

8. 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 8

9. 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 9

10. 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

11. Geometric Isomers in alkenes 3 or 4 substituents E/Z system
Br > F Cl > H
higher
lower Br F Cl H C
Zusamen – together (German)
(Z )-1-Bromo-2-chloro-1-fluoroethene 23

12. Geometric Isomers in alkenes 3 or 4 substituents E/Z system
Br > F Cl > H
lower
higher F Br Cl H C
Etgegen – opposite (German)
(E)-1-Bromo-2-chloro-1-fluoroethene 23

13. 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 outranks —CH3
—C(C,H,H)
—C(H,H,H) 24

14. 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) 26

15. Geometric Isomers in Cycloalkanes
Ring structures like C=C restrict rotation and therefore can result in cis and trans isomers 15

16. Properties of Geometrical Isomers
The chemical properties of geometrical isomers tend to be similar but their physical properties are different 16

17. Properties of Geometrical Isomers
The trans isomer has a much higher melting point. Unlike the cis isomer there is little intra-molecular hydrogen bonding 17

18. 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) 18

19. Optical Isomers
While these structures may look identical, in three dimensions they are mirror images of each other. Such molecules are called enantiomers. 19

20. Distinguishing Enantiomers
Optical isomers can be distinguished by the way they interact with plane polarized light

21. 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.

22. 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

23. 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.

24. Optical isomer limonene
(+) isomer strong smell of oranges/lemons
(-) isomer strong smell of pine needles/peppermint

25. Optical isomer Thalidomide
(+) isomer is a sedative (-) isomer is a teratogen

26. B.10 Stereochemistry in Biomolecules
Stereochemistry of biological molecules
2-amino acids
Carbohydrate
Fatty acids
Retinoids

27. 1) 2 – amino acids
All amino acids have a chiral centre except glycine.
All amino acid enantiomers are L-isomers
wedge-dash fischer projections

28. 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

29. 2-amino acids
L – enantiomers have amino group on the left D – enantiomers have amino group on the right

30. 2-amino acids - Position molecule so H atom at C-2 faces away
- 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

31. 2-amino acids

32. 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.

33. 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.

34. 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)

35. 2) Carbohydrates cyclic monosaccharides  -  system
or C-2 atom in fructose (ketoses = ketone)

36. 2) Carbohydrates cyclic monosaccharides  -  system
 tend to be more water soluble
The conversion b/n  and  occurs through open chain isomer

37. 2) Carbohydrates Cellulose  -  system
Cellulose is a polymer of -glucose, most abundant polysaccharides in plants.
Glucose residues are joined by -1,4-glycosidic links

38. 2) Carbohydrates Cellulose  -  system
Starch and glycogen are polymers of -glucose and are branched polymers
No branching in cellulose causes stronger intermolecular forces (H-bonds) 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

39. 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

40. 3) Fatty acids and triglycerides  -  system
- naturally occuring fatty acids have cis C=C, so not linear, weaker intermolecular forces, therefore cis-fats 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

41. 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.

42. 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

43. 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

44. 4) Retinoids Vitamin A
Opsin is a protein that can reversibly bind cis-retinal
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)

45. 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