Pharmaceutical Organic Chemistry 3 - Unit 2


Syllabus

Geometrical isomerism

Nomenclature of geometrical isomers (Cis Trans, EZ, Syn Anti systems)

Methods of determination of configuration of geometrical isomers.

Conformational isomerism in Ethane, n-Butane and Cyclohexane. Stereo isomerism in biphenyl compounds (Atropisomerism) and conditions for optical activity.

Stereospecific and stereoselective reactions



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POC-3 UNIT-2

GEOMETRICAL ISOMERISM

• The isomerism which arises due to restricted (frozen) rotation about double bond in molecules OR about single bond in cyclic compounds is known as geometrical or cis-trans isomerism.

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• Geometrical isomerism show by variety of compounds such as -

  • Compound containing double bond C=C , C=N , N=N
  • Compound containing cyclic structure
  • Restricted Rotation.

• Condition for geometrical isomerism -

i) There should be restricted (frozen) rotation about a bond in the molecules.
ii) Both substituents on each carbon about which rotation is frozen (restricted) should be different.

Screenshot 2026-04-05 172348

Nomenclature of Geometrical Isomers [Cis-Trans, EZ, Syn Anti System]

Geometrical Isomers can be nomenclatured by three methods

  1. Cis Trans Nomenclature
  2. E Z nomenclature
  3. Syn Anti Nomenclature.

1) Cis Trans Nomenclature

Compounds show this nomenclature due to restricted rotation about carbon-carbon double bond.

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  • Compounds should have atleast one double bond b/w carbon carbon.
  • Atleast one similar atom/group between both double bonded carbon.
  • Restricted Rotation.

Cis : The isomer in which the identical groups are on the same side of the double bond.

Trans : The isomer in which the identical group are on the opposite sides of the double bond.

examples \rightarrow

Screenshot 2026-04-05 173011


Screenshot 2026-04-05 173109


2) E Z Nomenclature

This nomenclature of geometrical isomers is more general and can be applied to all compounds.

  • Z (Zusammen \rightarrow together)
  • E (Entegegen \rightarrow Opposite)
  • It is based on Cahn-Ingold-Prelog system [Sequence Rule].
  • The group of highest priority on each carbon atom is identified by using the sequence rules

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(Z)-isomer (E)-isomer

  • (Z) - If the highest priority group are on the same side of the double bond.
  • (E) - If the highest priority group are on the opposite sides of the double bond.

Screenshot 2026-04-05 173323


3) Syn Anti Nomenclature

  • This type of nomenclature (isomerism) show by those compounds which have atleast one C=N or N=N.

    Syn \rightarrow Same
    Anti \rightarrow Opposite

    • Syn - If H on Carbon and substitute on Nitrogen are on same side.
    • Anti - When H on Carbon and substitute on Nitrogen are on opposite sides

Methods of determination of configuration of geometrical isomers

  • There are a number of methods to determine the configuration of geometrical isomers.
  • These are depending on the nature of the compounds.
    i) Physical method
    ii) Cyclisation method
    iii) Conversion method

i) Physical Method

  • The melting point and intensity of absorption of the cis-isomer are lower than those of the trans. Trans>Cis.
  • The boiling point, solubility, heat of combustion, heat of hydrogenation, density, refractive index, dipole moments and dissociation constant of the cis-isomers are greater than those of the trans. Cis>Trans.
  • So, By comparing these properties compound identified as cis or trans.

ii) Cyclisation Methods: (Methods of Cyclisation)

  • A cis isomers undergo cyclisation much more readily than the trans isomers.

    Example : Maleic acid forms a cyclic anhydride (maleic anhydride) when heated, whereas fumaric acid does not form fumaric acid anhydride.

    Screenshot 2026-04-05 173431


iii) Conversion Method: (method of conversion into compound of known configuration)

  • In a number of cases it is possible to determine the configuration of geometrical isomers by converting them into compounds of known configuration.

    Example:

Screenshot 2026-04-05 173529



Conformational Isomerism in Ethane, n-butane and Cyclohexane

Conformational Isomers

These are different spatial arrangements of a molecules that are generated by rotation about single bonds.

  • Use Newman Projection to these isomers.
  • The structure of conformers is of two types
    i) Staggered - Torsional angle is 6060^\circ.
    ii) Eclipsed - Torsional angle is 00^\circ.
  • Newman projection - Used to represent 3D structure.

  • Different conformations of the same molecules are sometimes called conformers/rotomer & conformational isomers.

  • Torsional angle - The angle between the atom attached to the front and rear carbon atoms. (Dihedral angle).

    Examples - Ethane [$CH_3-CH_3$]


1) Ethane

When an ethane molecule rotates about its carbon-carbon single bond, two conformations :- staggered and eclipsed.

  • Now, there are also use of energy during rotation.
  • Eclipsed conformation higher in energy than the staggered conformation.
  • There is some steric repulsion b/w the H atoms in the eclipsed conformation that is reduced in staggered conformation.

Due to this:
i) Eclipsed - least stable, extraa energy (torsional strain) - more internal energy
ii) staggered - Most stable, less internal energy.


  • Rotation

Screenshot 2026-04-05 173818

(I) (III) (V) \rightarrow Staggered (II) (IV) (VI) \rightarrow Eclipsed


  • ENERGY

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2) Butane

CH3CH2CH2CH3CH_3-CH_2-CH_2-CH_3

It has three carbon-carbon single bond and the molecules can rotate about each of them.

  • Rotation

Screenshot 2026-04-05 174045

It has six structure

(I, III, V) - staggered conformers
(II, IV, VI) - Eclipsed conformers


  • Conformer I - Most stable staggered, because in which two methyl group are as far (distance). \rightarrow Anti conformer (fully staggered).
  • Conformer III & V - Gauche conformer (partial staggered)
  • Conformer II & VI - Eclipsed (partial eclipsed)
  • Conformer IV - Fully eclipsed (least stable)

  • ENERGY DIAGRAM

Screenshot 2026-04-05 174151

\leftarrow stability \leftarrow fully staggered > Gauche > eclipsed > fully eclipsed.


3) Cyclohexane

  • Acc. to Sachce & Mohr, cyclohexane shows 2 forms of structure
  • Chair form \rightarrow staggered conformers (stable more).
  • Boat form \rightarrow eclipsed conformers (less stable).
  • Chair conformation is more stable than the boat conformation.

Screenshot 2026-04-05 174249


Energy diagram & Conformers

  • Conformations of cycloed cyclohexane are as follow

    i) Chair form
    ii) Half chair form
    iii) Twist boat form
    iv) Boat form


i) Chair Form

  • There is no steric hindrance, so it has minimum energy and maximum stability.
  • It is staggered conformers (most stable).

ii) Half chair form

  • It has both angle strain and torsional strain, so less stable than chair form.
  • Energy \rightarrow 46 kJ/mole.

iii) Twist boat form

  • More stable than boat conformation by about 5.4 kJ/mol, but less stable than chair conformation by 23.4 kJ/mol.

    Screenshot 2026-04-05 174349


iv) Boat form

  • Eclipsed conformers
  • There are steric interaction b/w the non-bonding atom due to this, the boat conformation is less stable than chair conformation and has higher energy content.

Screenshot 2026-04-05 174502



Stereo isomerism in biphenyl compounds (Atropisomerism) and conditions for optical activity

  • Atropisomerism : "Isolable stereoisomers resulting from restricted rotation about single bonds are called atropisomers and phenomena called as atropisomerism.

Atropisomerism \rightarrow Restricted Rotation around single bond $\rightarrow$ Stereoisomerism.

  • There is restricted rotation about the bond between the two phenyl rings due to steric hindrance between the bulky ortho substituents.
  • These phenyl rings lie in different planes which are perpendicular, thus the molecules becomes chiral and exhibits enantiomers.

Screenshot 2026-04-05 174610

  • Conditions for optical activity & for atropisomerism.

    i) There should be any functional group/atom at ortho position of rings [substitution at ortho position with large size such as - Cl, Br, I, COOH, NO2, SO3H, CH3 etc-].

    ii) Each ring must be resolvable, for that aba \neq b and cdc \neq d.

Examples

Screenshot 2026-04-05 174656

Biphenyl atropisomers



Sterospecific and Stereoselective reaction

1) Stereospecific Reaction : [stereospecific synthesis]

  • A reaction in which a particular stereoisomer react to give one specific stereoisomer of the product.
  • In this reaction, stereoisomers gives different stereoisomere product. (stereospecificity). ea

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Screenshot 2026-04-05 174928

Cis (Reactant) (Product) Trans

Trans (Reactant) (Product)


2) Stereoselective Reaction: [stereoselective synthesis]

  • A reaction in which two or more stereoisomers formed possibly, but one stereoisomers is obtained more than the other.

Example :

Screenshot 2026-04-05 175036


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Unit 2, Pharmaceutical Organic Chemistry 3, B Pharmacy 4th Sem, Carewell Pharma
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