Supramolecular Chemistry

Prof. (Mrs) Farukh Arjmand

Department Of Chemistry
Co-Director , APJ Abdul kalam Indo-US STEM-ER centre
Aligarh Muslim University, Aligarh. AMU
Email id: [email protected]

27th August'19 MOOC (LeAP) UGC HRDC

 Supramolecular Chemistry

Supramolecular chemistry may be defined as ―chemistry beyond

the molecule‖, bearing on the organized entities of higher
complexity that result from the association of two or more
chemical species held together by intermolecular forces.
In supramolecular chemistry, noncovalent interactions occur
between molecular building blocks, which by molecular
recognition and self-assembly form (functional) supramolecular
entities.
It is also termed the ―chemistry of the non-covalent bond.‖

27th August'19 MOOC (LeAP) UGC HRDC

 Basic Principles
Non-covalent Interactions
Bonding interaction that cannot be described in terms of classical ―electron sharing
between two atoms by the overlap of two atomic orbitals to form molecular orbitals.‖
Noncovalent interactions are weak dispersion, dipole–dipole, cation–π interactions,or
π–π stacking and quite strong electrostatic, coordinative interactions.

Molecular recognition
Molecular recognition is the specific interaction between two molecules, which are
complementary in their geometric and electronic features (like two fitting pieces of a
jigsaw puzzle).

Self assembly
Recognition between molecules leads to an aggregation, which finally results in an
ensemble that is composed of two or more discrete units which possess special
properties or supramolecular functions, which are only found in the ensemble but not
in the participating molecules.
27th August'19 MOOC (LeAP) UGC HRDC
Essential biological processes, e.g., reproduction, signal
transduction, information storage, and processing are all based
on supramolecular interactions between molecular components.
Enzymes, viruses, membranes, and many other complicated
structures with biologically relevant functions are mainly built
up by simple self-assembly processes.
The processes can be mimicked in small artificial supramolecular
derivatives.

27th August'19 MOOC (LeAP) UGC HRDC

 Polymolecular

From Molecular to Supramolecular Chemistry Organized assemblies

Molecular & Supramolecular Devices

Translocation
A B
Transformation

Recognition
Synthesis
Receptor
Covalent bonds Complexation
Supermolecule
Intermolecular
Bonds
C D Substrate
MOLECULAR SUPRAMOLECULAR

CHEMISTRY
 Molecular Recognition

 Molecules that interact physically and react chemically in specific and

selective ways are the basic constituents of this living world. This is called the
molecular recognition process and it controls the formation of multi
molecular assemblies

 Molecular recognition is the specific interaction between two molecules,

which are complementary in their geometric and electronic features (like two
fitting pieces of a jigsaw puzzle).

 By the use of this principle we can construct large ensembles of molecules.

The most sophisticated and effective examples of self assembly occur in living
systems.

27th August'19 MOOC (LeAP) UGC HRDC

 The pieces of the puzzle fit together, if
they are complementary in shape
(molecular recognition) and if this
process is reversible (non-covalent
interactions, the best-fitting result is
favored. By connecting all the pieces
of the jigsaw puzzle in the correct way
(self assembly) the final object is
obtained (a). Wrong connections lead
to an unfavored and thus more unstable
entity (b), which is eventually
disconnected again to arrange the
pieces correctly.
Schematic representation of self-assembly of a supramolecular aggregate by molecular
recognition and non-covalent interactions ( Jigsaw puzzle model)
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 Applications of Molecular recognition
 Sensor technology
 Molecular electronics- switches, transistors and
molecular wires
 Molecular magnetic devices
 Photo-chemical molecular devices
 Catalysis
 Drug design

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9
 Synthetic Strategy

To construct supramolecules, the initial step involves the covalent synthesis

(organic synthesis) to construct subunits which by non-covalent bonds can
aggregate with themselves or other synthetic subunits to afford stable,
structurally defined surface molecular assemblies. The lock and key
principle describes the fit of a rigid substrate to a rigid receptor analogous
to a key and a lock. Mechanically interlocked molecules like rotaxanes (a
ring fixed on a terminally blocked axis), catenanes (two intertwined rings),
and also molecular knots (e.g., trefoil knots) are considered as
supramolecular species. The partners of a supramolecular species
have been named molecular receptor and substrate , the substrate being
usually the smaller component whose binding is being sought.
27th August'19 MOOC (LeAP) UGC HRDC
Figure 1. Synthetic strategy based on self assembly: Conversion of
simple building blocks, which can assemble into complex chemical
entities

27th August'19 MOOC (LeAP) UGC HRDC

An example of supramolecular assembly worth mentioning is the
construction of rotaxane (a class of molecules in which a dumbbell
shaped component is encircled by a macrocycle). The two
components are linked by a non-covalent interaction. The complex
formed between these two species can then be modified with
blocking groups to produce the [2] rotaxane. The prefix [2] indicates
the number of mechanically linked components within the molecule.

Figure 2. Schematic representation of the synthesis of a [2] rotaxane

by threading 27th August'19 MOOC (LeAP) UGC HRDC
Ogino and coworkers, reacted diaminoalkanes with α-
cyclodextrin (α- CD) or β CD which after the formation of
inclusion complex further reacted with the cobalt complex
[CoCl2(en)2] (en = ethylenediamine ) yielding [2] rotaxane.

Figure . Cyclodextrin rotaxanes constructed from α,ω diaminoalkanes and

cobalt based blocking groups
27th August'19 MOOC (LeAP) UGC HRDC
The supramolecular chemistry has its own terminology, like
ligands in coordination compounds, the supramolecular
compounds have been named as receptor (ρ) and substrate (σ)
[being smaller component].

The selective binding of a specific substrate σ to its receptor ρ

yields supramolecule ρσ and involves molecular recognition
process. In addition to binding sites, if a receptor also bears
reactive functions, it may affect a chemical transformation on the
bound substrate thus behaving as a supramolecular reagent or
catalyst.

27th August'19 MOOC (LeAP) UGC HRDC

Naming of such compounds poses some specific problems.
Receptors and substrates themselves are covalent structures
whose naming is governed by rules approved in the Geneva
conference.
Conventions used for coordination compounds may be a starting
point e.g; κ, kappa (indicating coordinating atom), hapto, η
(for coordinated group) or μ (for bridging ligands).
 Spatial localization of bound substrate with respect to the
receptor also requires some formalism. External addition
complexes may be written as [A, B] or [A//B] , the mathematical
symbols of inclusion € and intersection ∩ have been introduced.
Requirements for the design of supramolecular
system
Steric factors (shape and size) presence of convex and concave
domains in substrate and receptor molecules.
Interactional complementarity (which depends on well-defined 3-
D architecture with correct arrangement of binding sites),
Large contact areas between receptor and substrate.
Multiple interaction sites
Strong overall binding
medium also plays an important role through the interaction of
solvent molecules with receptor and substrate as well as with each
other.
Recognition implies the geometrical and interactional
complementarity, i.e; presence of complementary binding
sites (electrostatic such as positive/negative,
charge/dipole, dipole/dipole, hydrogen-bond,
donor/acceptor etc.) between the associating partners.

Base pairing Adenine and H-bonded barbiturate with 2,6-pyridine

thymine(A-T) diamide groups
 Different types of Molecular receptors
The simplest recognition process is that of spherical substrates; these are
either positively charged metal cations (alkali, alkaline-earth, lanthanide
ions) or the negative halide anions. cryptands as well as related compounds
display spherical recognition of appropriate cations and anions. Their
complexation properties result from their macropolycyclic nature and
define a cryptate effect characterized by high stability and selectivity, slow
exchange rates and efficient shielding of the bound substrate from the
environment.
For further reading
• Supramolecular Chemistry-Scope and perspectives
-Jean-Marie Lehn, Noble lecture, December 8, 1987.
• Supramolecular chemistry—general principles and
selected examples from anion recognition and metallo
supramolecular chemistry.
- M. Albrecht, Naturwissenschaften (2007) 94:951–966