Stereochemistry

-- a subdiscipline of chemistry, which involves the study of the relative spatial

arrangement of atoms that form the structure of molecules and their manipulation.
 Chirality

Mirror
Chirality came from Greek “Kheir”
means hand
Chiral molecule: A molecule or an object is said to be chiral if it is
not superimposable on its mirror image. E.g., human right palm
and left palm.

Chiral centre: A centre contains four different groups or atoms.

Chiral molecule: Lactic acid.
Chiral centre
three two
• Due to free rotation along the central bond, two conformations are
possible – the staggered and eclipsed.
Rear
Carbon CO2H
H OH
Rotation by 180°
along C2-C3 bond HO H
HO
H HO
CO2H H

CO2H CO2H
Eclipsed Staggered

Sawhorse Projection
 H Br

CH3
CH3
H Br
Br H
Br H

CH3 CH3

Eclipsed Fischer Projection

Sawhorse Projection
Conformational analysis: Conformations of
n-butane
Di
Isomerism
Types of Isomerism
Structural Isomers
 Structural Isomers
CHAIN ISOMERISM
Structural Isomers
 Structural Isomers
Tautomerism:
Isomerism due to interconvert of one compound to another by
relocation of H-atom within the molecule.
 Stereoisomers

Enantiomers - Mirror images

 Diastereomers
Diastereomers are stereoisomers that are not mirror images of each other and non-
superimposable. Diastereomers can have different physical properties and reactivity.
They have different melting points and boiling points and different densities. They
have two or more stereocenters.
Chiral Molecules, Optically Inactive – Racemic Mixture
Optical Activity
Optical Rotation
Optically Active
Meso-Compound – Optically Inactive
Configuration
 Sequence Rules -- Cahn, Ingold, Prelog
 The Cahn–Ingold–Prelog (CIP) sequence rules, named for organic chemists Robert
Sidney Cahn, Christopher Kelk Ingold, and Vladimir Prelog — alternatively termed
the CIP priority rules, system, or conventions — are a standard process used in
organic chemistry to completely and unequivocally name a stereoisomer of a
molecule.

 The purpose of the CIP system is to assign an R or S descriptor to each

stereocenter and an E or Z descriptor to each double bond so that the
configuration of the entire molecule can be specified uniquely by including the
descriptors in its systematic name.
 Sequence Rules -- Cahn, Ingold, Prelog
Steps for naming
 The steps for naming molecules using the CIP system are often presented as:

 Identification of stereocenters and double bonds;

 Assignment of priorities to the groups attached to each stereocenter or double-
bonded atom
 Assignment of R/S and E/Z descriptors.
 Sequence Rules -- Cahn, Ingold, Prelog
Assignment of priorities
R/S and E/Z descriptors are assigned by using a system for ranking priority of the groups
attached to each stereocenter. This procedure, often known as the sequence rules, is the
heart of the CIP system.

1. Compare the atomic number (Z) of the atoms directly attached to the stereocenter; the
group having the atom of higher atomic number receives higher priority.

2. If there is a tie, we must consider the atoms at distance 2 from the stereocenter—as a
list is made for each group of the atoms bonded to the one directly attached to the
stereocenter. Each list is arranged in order of decreasing atomic number. Then the lists
are compared atom by atom; at the earliest difference, the group containing the atom
of higher atomic number receives higher priority.

3. If there is still a tie, each atom in each of the two lists is replaced with a sublist of the
other atoms bonded to it (at distance 3 from the stereocenter), the sublists are arranged
in decreasing order of atomic number, and the entire structure is again compared atom
by atom. This process is repeated recursively, each time with atoms one bond farther
from the stereocenter, until the tie is broken.
Assignment of priorities
Assign R/S configuration for each of the following molecules

S R

R
Achiral – R/S NA
3 1
C

2 CH
S C CH2
H C
(C, C, H)
CH2
HC
OH C
C
C CH3
H C C
C CH

C
(C,C,C)
 Relative Configuration

d l

l
• ISOMERISM IN COORDINATION CHEMISTRY
 Structural Isomerism
1. Ionization isomerism
2. Hydrate isomerism
3. Coordination isomerism
4. Linkage isomerism
 Ionization isomerism:
• Same overall Composition. But the composition of the coordination sphere
varies.
• Some isomers differ in what ligands are bonded to the metal and what is
outside the coordination sphere; these are also called coordination-sphere
isomers.

• [Cr(NH3)5SO4]Br and [Cr(NH3)5Br]SO4

• Here, the counter ions (anion) are different. In the former, sulfate
coordinates to metal and bromide is counter ion. In the latter one, opposite
happens.
• Upon ionization, or upon dissolution in water, we get bromide anion in the
former case, where as, we will get sulphate anion in the latter case.
 Hydrate (or solvate) isomerism

• Three isomers of CrCl3(H2O)6 are

• The violet [Cr(H2O)6]Cl3,
• The green [Cr(H2O)5Cl]Cl2 ∙ H2O, and
• The (also) green [Cr(H2O)4Cl2]Cl ∙ 2H2O.

 Coordination isomerism
• They differ in coordination entities
• For example, [Co(NH3)6][Cr(CN)6] and [Co(CN)6][Cr(NH3)6] are coordination
isomers.
[Co(NH3)6]3+ & [Cr(CN)6]3- [Cr(NH3)6]3+ & [Co(CN)6]3-

• They have same total compositions, but they have different complex entities
(complex ions).

• Another example: [Zn(NH3)4][CuCl4] and [Cu(NH3)4][ZnCl4] compounds are also

coordination isomers.
 Linkage Isomerism
• Composition of the complex ion is the same, but the point of attachment of
at least one of the ligands differs.
• The donor atom of ligand varies

 Linkage Isomerism of NO2–

Same ligand, but the donor Nitro- Nitrito-

atom is different

 Linkage Isomerism of thiocyanate (SCN−) & isothiocyanate (NCS−)

• linkage isomers are violet-coloured

[(NH3)5Co(SCN)]2+ and orange-
coloured [(NH3)5Co(NCS)]2+

Violet Orange
 Trans- and Cis- isomers of Square Planar Complexes
 With these geometric isomers, two
chlorines and two NH3 groups are
bonded to the platinum metal, but
are clearly different.
 cis-Isomers have like groups on the
same side.
 trans-Isomers have like groups on
Cis-[Pt(NH3)2Cl2] Trans-[Pt(NH3)2Cl2] opposite sides.
Cis-Platin Trans-Platin

 Number of each atom is the same, the mode of bonding the same, but the arrangement
in space is different

 Cis-platin is used to treat various types of cancers. Where as, the trans-form does not
exhibit a comparably useful pharmacological effect.