Pharmaceutical organic chemistry 3 B.pharm IV SEM

1. NOMENCLATURE OF
OPTICAL ISOMERS

2. Representation of structure of molecules
1. Wedge and Dash Projection:
❑ These are the 3D representation of molecules.
❑ These are used for both chiral and achiral molecules.
❑ This projection is used for tetrahedral structure, in which two atoms/ groups
are in plane and other two groups are in above or below plane.
Eg: Glyceraldehyde

3. Representation of structure of molecules
2. Fischer Projection:
❑ It is developed by Emil Fischer in 1891.
❑ It is the 2D representation of molecules.
❑ In this, all bonds are drawn as solid lines.
❑ In this method, carbon chain is always written vertically and horizontal
lines represent other groups.
❑ Below the plane- right side; Above plane- left side.
Eg: Glyceraldehyde

5. OPTICAL ISOMERISM
CONFIGURATION
❖ Configuration means the arrangement of atoms or groups around
the asymmetric centre
❖ Two system have been developed
I. Relative configuration
D and L – system of nomenclature
II. Absolute configuration
R and S – system of nomenclature

6. D and L – SYSTEM OF NOMENCLATURE
➢ This is one of the oldest and the most commonly used system for assigning configuration to a given
enantiomer.
➢ This was developed by Fischer and Rosanoff around 1900.
➢ Fischer first developed a method for drawing carbohydrates in two-dimensions and a convention with
respect to orientation so as to indicate their three dimensional structures, so-called Fischer
projections.
➢ Fischer and Rosanoff then devised a notation for designating the configurations of stereogenic
centres, depicted in Fischer projections, as either D or L.
➢ This nomenclature is based upon the comparison of the Fischer projection formula of one enantiomer to
which the name is to be assigned, with that of a standard substance arbitrarily chosen for comparison.
➢ The following two conventions are used for this purpose.
(i) Hydroxy Acid or Amino Acid Convention
(ii) Sugar Convention

7. (i) Hydroxy Acid or Amino Acid Convention
• According to this convention the prefix D and L refers to the configuration of
α-hydroxy or α-amino acids (i.e. the lowest numbered chirality centre) in the
Fischer projection formula.
• If the α-OH or α-NH2 group is on the right hand side (of the viewer), the
prefix D is used.
• Whereas if α-OH or α-NH2 group are on the left hand side the prefix L is
used.

8. Add a Slide Title - 2

9. (ii) Sugar Convention
• Fischer arbitrarily assigned D and L configurations to (+) and (–)-
glyceraldehyde, respectively.
• He assigned D configuration (OH on the right) to (+) -glyceraldehyde and L
configuration (OH on the left) to (–) -glyceraldehyde.

10. • The enantiomer that can be prepared from or converted to D (+)
glyceraldehyde will belongs to D-series.
• Similarly any compound that can be prepared from or converted to L (-)
glyceraldehyde will belongs to L-series.
• NOTE: D & L are configurational symbols so there can be D (+/d) & D (-/l)
compounds, similarly L (+/d) & L (-/l) compounds.
• Eg:

11. SEQUENCE RULES
➢ Sequence rule is important for assignment of configuration to chiral centres.
➢ It is used for assignment of R & S configuration and E & Z Prefixes.
➢ Sequence rule 1: if the four atoms attached to the chiral centre are all
different, priority depends on atomic number, with the atom of higher
atomic number getting highest priority.
➢ Eg:
Higher atomic number –
highest priority
I> Cl> S> H

12. • If two atoms are isotopes of the same element, the atom of
higher mass number has the highest priority.
Br> C> D> H

13. Sequence rule 2:
❖ If the relative priority of two groups cannot be decided by
rule 1, it can be determined by a similar comparison of the
next atoms in the groups.
❖ That is, if two atoms attached to the chiral centre are the
same, compare the second atoms (first point of difference).
❖ Eg: In sec- butyl chloride, two of the atoms attached to the
chiral centre are themselves carbon.
❖ In CH3, second atoms are H,H,H
❖ In C2H5, second atoms are C,H,H.
❖ Since carbon has higher atomic number than hydrogen,
C2H5 has the highest priority.
Cl> C2H5> CH3> H

14. Sequence rule 3:
➢ Where there is a double or triple bond, both atoms are considered to be
duplicated or triplicated.
➢ It should be treated as if it were singly bonded to two or three of those atoms
respectively.
➢ Eg: In Glyceraldehyde, OH group has highest priority of all and O,O,H of –CHO takes
priority over the O,H,H of –CH2OH.
-OH> -CHO> -CH2OH> -H
Glyceraldehyde

15. R and S – System of nomenclature
(CIP SYSTEM)
• R and S system was devised by R. S. Cahn, Christopher Ingold and Vladimir Prelog (CIP).
• The Cahn-Ingold-Prelog convention is used to identify the configuration of each asymmetric
carbon atom present in a stereoisomer.
• Assigning the Absolute Configuration
STEP I: Use the Cahn-Ingold-Prelog priority rules to assign priority (one through four) to the
four groups on the chiral atom.
STEP II: Orient the molecule so that the lowest priority atom is in the back (away from you).
Look at the remaining three groups of priority 1-3.
If the remaining three groups are arranged so that the priorities 1>2>3 are in a clockwise direction,
then assign the chiral center as R (“rectus” or right).
If the remaining three groups are arranged 1>2>3 in a anti-clockwise manner, then assign the
chiral center as S (“sinister” or left).

16. R,S – SYSTEM OF NOMENCLATURE
Step I: According to sequence rule (priority)
Rule 1: If the four atoms attached to the chiral centre are all different, priority
depends on atomic number, with the atom of higher atomic number getting
highest priority.
I> Br> Cl> H

17. Rule 2: If two atoms are isotopes of the same element, the atom of
higher mass number has the highest priority.
Br> C> D> H

18. • Rule 3: If the relative positions of two groups cannot be
determined as earlier, they are decided by a comparison of priority
atom at the first point of difference.

19. Rule 4: Where there is a double or triple bond, both atoms are considered to
be duplicated or triplicated.
➢ It should be treated as if it were singly bonded to two or three of those
atoms respectively.
➢ Eg: In Glyceraldehyde, OH group has highest priority of all and O,O,H of
–CHO takes priority over the O,H,H of –CH2OH.
-OH> -CHO> -CH2OH> -H
Glyceraldehyde

20. Step II: According to orientation of molecule
1. Assign priorities to four different atoms attached to chiral centre based on their
atomic number.
2. Trace a circle from 1 to 2 to 3
3. Determine the orientation of 4 priority group.
If it is orientated into the plane of paper (away from you), follow step 4a.
If it is orientated out of the plane of paper (toward you), follow step 4b.
4a. 4 group pointing away from you: clockwise direction – R configuration;
anticlockwise direction- S configuration.
4b. 4 group pointing toward you: configuration is reversed.
clockwise direction – S configuration; anticlockwise direction- R configuration.

21. • Eg- 4a • 4b

22. Absolute configuration of Fischer Projection
(Golden Rule)
❑ Step 1: Assign priority to four groups bonded to the chiral centre using CIP priority system.
❑ Step 2:
a) Vertical position
❑ If the lowest priority group is on a vertical bond: clockwise direction – R configuration;
anticlockwise direction- S configuration.

23. Absolute configuration of Fischer Projection
(Golden Rule)
b) Horizontal position
❑ If the lowest priority group is on a horizontal bond: clockwise direction – S configuration;
anticlockwise direction- R configuration.

24. Interchanging between groups
I. In Fischer projection, the least priority number is not
at the bottom of the plane.
• In such cases, the Fisher projection formula of the
compound is converted in to another equivalent
projection formula in such a manner that atom the
lowest priority is placed vertically downward.
• This may be drawn by two interchanges between
four priority numbers. The first interchange involves
the two priority numbers, one is the least priority
number and the other is the priority number which is
present at the bottom of the plane.
• Second interchange between remaining groups.
• clockwise direction – R configuration; anticlockwise
direction- S configuration.

25. II. If the group of lowest priority is not bonded by dashed line then interchange a
pair of groups so that the group with the lowest priority is bonded by dashed line.
• Now see the sequence (1 2 3), if it is clockwise then the configuration is
assigned as S and if anticlockwise as R.
Interchange 3
and 4
Clockwise
direction - S

26. SUMMARY
Orientation of molecule Away from you Towards you
Clockwise direction R S
Anticlockwise direction S R
Interchanging group rule Fischer formula Flying wedge formula
Clockwise direction R S
Anticlockwise direction S R
Fischer formula (Golden rule) Vertical bond Horizontal bond
Clockwise direction R S
Anticlockwise direction S R

27. IMPORTANCE OF ENANTIOMERS AS
CHIRAL DRUGS:
• Eg:

28. Pain killer
more active
Less active
Beta blocker Inactive