Supramolecular chemistry

Supramolecular Chemistry THOSHINA THOMAS

KEYI SAHIB TRAINING COLLEGETALIPARAMBA

Supramolecular chemistry, a term introduced by Jean-Marie Lehn, is “chemistry beyond the molecule”,i.e. the chemistry of molecular assemblies using noncovalent bonds.

Nobel Prize in 1987: Pederson C , Cram D J, Lehn J M.

Introduction:

In 1967, Pedersen observed that crown ether showed

molecular recognition – the first artificial molecule found

to do so.

Cram established, host–guest chemistry, where the

host molecule can accommodate another guest

molecule.

In 1978, Lehn proposed the term “supramolecular chemistry”.

Together, Pedersen, Cram and Lehn received the

Nobel Prize for Chemistry in 1987.

Lessons from nature--DNA bound by base pairs

Supramolecular chemistry – in nature

Introduction:

“Supramolecular chemistry” - “chemistry beyond the molecule”

According to Dr. Lehn, who invented the term, a supermolecule formed by the association of two or more chemical species held together by intermolecular forces. Like..

hydrogen bonding, hydrophobic interactions and coordination.

• focuses on non-covalent bonding interactions focuses on non-covalent bonding interactions of molecule.of molecule.

• Forces include hydrogen bonding, metal Forces include hydrogen bonding, metal coordination, Van der Waals forces, pi-pi coordination, Van der Waals forces, pi-pi interactions, electrostatic effects…interactions, electrostatic effects…

Intermolecular and intramolecular forces

Intermolecular BondingBonding between molecules

van der Waals forces• Hydrogen bonding

– This relatively strong type of inter-molecular bonding between a hydrogen atom and an electron pair or electronegative atom.

– Multiple hydrogen bonds hold the DNA double helix together.

• Dipole interaction• London forces

– These are induced forces caused by a temporary rearrangement of the electron clouds when molecules bump together.

Supramolecular chemistry – the forces

Hydrogen Bonding H

OHO

H

H

OH

H

Dipole Interaction• The partial positive and negative ends of

the molecules hold the molecules together.

London Dispersion Forces (LDF)

instantaneous dipole–induced dipole forces, London forces are induced dipoles caused by temporary rearrangement of the electron cloud.

Assembled by π-π interaction

Some simple models:

Cation–π interaction bn benzene and a

Na cation.

Polar π interaction bn water molecule and benzene

Π - π interaction bn e rich benzene

& e poor hexafluorobenz

ene

http://en.wikipedia.org/wiki/Benzene

http://en.wikipedia.org/wiki/Cation

Assembled by metal-ligand

P. J. Stang, Chem. Eur. J., 1998, 4, 19-27


Nanosized cavities.

J. Manna, P. J. Stang, J. Am. Chem. Soc. 1996, 118, 8731.


Twelve units come together precisely with high yield: A Remarkable reaction

P. J. Stang, N. E. Persky, J. Manna, J. Am. Chem. Soc. 1997, 119, 4777.

Classification of Supramolecules

molecular recognition chemistry

chemistry associated with a molecule recognizing a

partner molecule

chemistry of molecules

built to specific shapes

chemistry of molecular

assembly from numerous molecules “lock and key”

host–guest chemistry

Molecular recognition chemistry (host–guest chemistry) + chemistry of molecular assemblies + chemistry of molecular associations “supramolecular chemistry”

[Amphiphilic molecules –

micelles, lipids..]

[Rotaxane, catenane, Dendrimers,

Fullerene, CNTs..] [Crown ether, Polyamines, Cyclodextrin, calixarne..]

“lock and key”

Host-guest chemistry

Supramolecular chemistry – lock-and-key

Different Supermolecules

Chemists Interested In Such systems

Early 1970 molecular recognition in biological systems attracted synthetic chemists.

1967 discovery of crown ethers.

(Charles Pederson).

As 0.4% impurity !

[18] crown-6 a host for K+

Host-Guest chemistry is an example of supramolecular chemistry.

Molecular assembly!? Human made DNA

Chemical level

Host Molecules

1) Crown Ethers:

Crown ethers were the first artificial host molecules discovered. They were accidentally found as a byproduct of an organic reaction. When Pedersen synthesized bisphenol, contaminations from impurities led to the production of a small amount of a cyclic hexaether

Pedersen called the cyclic compound a crown ether, because the cyclic host “wears” the ion guest like a crown.

Crown ethers are named as follows: the number before “crown” indicates the total number of atoms in the cycle, and the number after “crown” gives the number of oxygen atoms in the cyclic structure. The oxygen atom, which has a high electronegativity, can act as a binding site for metal ions and ammonium ions through dipole–ion interactions.

Crown ethers are classified by structural types: noncyclic hosts are known as podands; monocyclic hosts including crown ethers are called coronands; oligocyclic hosts are termed cryptands.

Cryptands have a motion-restricted cyclic structure; they can accommodate only strictly size-matched guest molecules.

2) Macrocyclic Polyamines – Nitrogen-Based Cyclic Hosts:

Replacing the oxygen atoms in the crown ethers by nitrogen atoms - macrocyclic polyamines.

Strong basic nature of the amine group results in unique host properties.

Thioether-type crown compounds (crown ethers with sulfur atoms instead of oxygen atoms) are called as thiacrowns.

3) Cyclodextrin – A Naturally Occurring Cyclic Host:

Cyclodextrins can be obtained from starch (polysaccharide with an α 1–4 linkage of glucose) via certain enzymes.

The enzyme changes this polysaccharide into a cyclic oligomer with an appropriate number of glycopyranoside units.

6,7,8 glycopyranside units (are called α-, β- and γ -cyclodextrin, respectively)

Structural design:

Primary hydroxyl groups are located at the side of a narrow inlet,

while secondary hydroxyl groups are found on the reverse side (at

the side of a wide inlet).

Therefore, no hydroxyl groups exist on the wall, and so the cavity of

the cyclodextrin is hydrophobic.

Cyclodextrins dissolved in an aqueous phase can accommodate

hydrophobic guests such as aromatic hydrocarbons (benzene),

inorganic ions & gas molecules in their cavities.

Structure of a cyclodextrin and some pore diameters

Dimer naphthalene formation results in stronger emission

Inclusion of a guest inside the cavity of a cyclodextrin induces light emission

Hydrolysis of phenyl acetate by cyclodextrin to phenol & acetate

artificial enzyme, where a cyclodextrin cavity works as a hydrophobic binding site and hydroxyl groups play the role of a catalytic residue.

4) Calixarene– A Versatile Host:

Calixarenes are macrocyclic host molecules made from phenol units linked through methylene bridges.

name “calixarene” reflects the structures of these molecules, since a calix is a chalice (trophy).

Calix[n]arene

Calix[4]arene

Calixarenes:

macrocycles that are made from phenol or P-tert-butylphenol.

Calix[4]arene Calix[8]areneCalix[6]arene

Different views of calix[4]arene

~ 3-7 Å width

The isomers vary in terms of the orientations of their phenol groups:

(a)has a cone structure with all of the phenols pointing to the same direction;

(b) has a partial cone structure with one phenol pointing in a different direction to the others;

(c) has a 1,3-alternate structure with neighboring phenols pointing in opposite directions.

Confirmation isomers of Calix[4]arene

The calix[8]arene depicted in Fig. can bind fullerenes

Binding of fullerene by Calix[8]arene

The calix[8]arene has a cavity with an inner diameter of 1nm, which is ∼therefore suitable for C60, since it has a diameter of 0.7nm. So in the ∼figure 10 we can see the fullerene “soccer ball” is trapped in the calix.

5) Cyclophane– 3 dimensinal cavitied Host:

Cyclophanes are cyclic hosts made from aromatic rings that recognize hydrophobic guest molecules. Three dimensional cavities can be constructed by attaching tails, walls and caps to the cyclic hosts.

Endoreceptors and Exoreceptors

According to Lehn’s definition, host molecules that have binding sites inside their molecular structures (cavities) are called endoreceptors.

For example, enzymes are generally endoreceptors, because they recognize the guest substrate in a reaction pocket located inside the enzyme.

Host molecules with guest binding sites on their surfaces are defined as exoreceptors.

Antibodies are classified as the exoreceptors because they recognize antigen on the terminal surface.

Classification of Supramolecules

molecular recognition chemistry

chemistry associated with a molecule recognizing a

partner molecule

chemistry of molecules

built to specific shapes

chemistry of molecular

assembly from numerous molecules “lock and key”

host–guest chemistry

Molecular recognition chemistry (host–guest chemistry) + chemistry of molecular assemblies + chemistry of molecular associations “supramolecular chemistry”

[Amphiphilic molecules –

micelles, lipids..]

[Rotaxane, catenane, Dendrimers,

Fullerene, CNTs..] [Crown ether, Polyamines, Cyclodextrin, calixarne..]

Medium-size with Specific shape supermolecules

These supermolecules have interesting and unique geometric features.

Some examples (are nanoparticles) include

Fullerenes,

Carbon nanotubes,

Dendrimers,

and Rotaxanes, Catenanes etc.

1. FULLERENES

• One example is the Buckminsterfullerene (Buckyball)

• It has a formula C60

• It is a black solid

• Dissolves in petrol to make ared solution

• Free moving electrons so conducts electricity

They are spheres of only carbon atoms and are also allotropes of carbon

Buckminsterfullerene C60, also known as the buckyball, is the smallest member of the fullerene family.

Metal-doped fullerene can therefore be regarded as a “superatom”. Doped fullerenes are also known to exhibit superconductivity.

C60 Metal-doped fullerene

CARBON IN DIFFERENT DIMENSIONS

3 D CARBON

2 D CARBON

Graphene

Iijima, 1991

NANO TUBES ARE TINY TUBES OF CARBON ABOUT 10,000 TIMES THINNER THAN HUMAN HAIR.

THESE CONSIST OF ROLLED UP SHEETS OF MULTI LAYER CARBON ATOMS IN HEXAGON SHAPE.

THEY CONDUCT ELECTRICITY BETTER THAN COPPER AND ARE MORE STRONGER THAN STEEL WIRE .

Carbon nanotubes can store huge volumes of gas

Carbon nanotubes can also be used as tips in probe microscopy.

Single wall Nanotubes Multi wall Nanotubes

Preparation

Preparation of nanomaterials is commonly referred as Nanofabrication.

Two approaches used for fabricating to nano scale particles are Top-down nanofabrication and Bottom-up nanofabrication.

Top-down method involves carving bulk to desired size.

Techniques used to perform this method are Precision Engineering and Lithography.

The bottom-up method involves building up of materials atom by atom or molecule by molecule.

Positional assembly and Self-assembly, are the techniques

TOP DOWN methodFrom large to smallNanoscale structures by cutting down materials to smaller and smaller sizes

BOTTOM UP methodFrom small to large Things are made by building up from the atomic scale.

How to make nanomaterials

3. Dendrimers – Molecular Trees

Dendrimers have systematic branching structures and they are built in a stepwise manner.

The word “dendrimer” contains “dendr-”, which means tree. So it can be treated as a molecular trees

or they are nano sized polymers.

Dendrimers are constructed by stepwise connection of several parts (divergent method and convergent method).

Porphyrin unit immobilized in a

dendrimer

Dendrimer Porphyrin

Star-shaped dendrimers can also be synthesized, using stepwise dendrimergrowth and subsequent linear polymerization

4. Rotaxanes–Threading Molecular Rings

Rotaxanes are obtained by threading linear polymers through molecular rings such as cyclodextrins, crown ethers and cyclophanes.

The word “rotaxane” means wheel axle (rota = wheel, axis = axle). Structurally, they consist of molecular rings threaded by molecular wires that have stoppers at both ends to keep the rings in place.

When more than one ring is threaded by a single wire, the structure is called a polyrotaxane. Sometimes we encounter a rotaxane with no stoppers; these molecules are called pseudo-rotaxanes.

These structures occur in naturally-occurring systems (some DNA enzymes are ring-shaped, and the DNA chain passes through the enzyme ring).

In 1960s researchers discovered artificial rotaxane structures by stepwise process

Cyclodextrin-based rotaxane

5 Catenanes– Complex Molecular Associations

Catenanes consist of two or more interlocked rings. (Latin word “catena”, means linked chains.)

Although the interlocked rings in catenanes are not bonded together by covalent bonds, they cannot be separated from each other.

Strategies for catenane synthesis

Molecular Self Assembly –Building Supermolecules

Supramolecular assemblies- The supermolecules result

from self-assembling (or self-organizing) processes.

Molecular Self Assembly –Building Supermolecules

fuzzy molecular interaction.

programmed assembly(precisely defined

recognition)

Programmed Supramolecular Assembly: Precise…

For example, the three-dimensional structures of proteins are defined by their amino acid sequences; in other words, the structure of a protein is programmed in its amino acid sequence.

Supramolecular Assembly via Fuzzy Interactions:

Fuzzy (unclear or un precise) interactions, sometimes produce more flexible, sensitive and adaptable functionality.

Eg. cell membranes,

Supramolecular chemistry – self assembly

Programmed Supramolecular Assembly

“Precisely programmed” structural information in the unit structure.

For example,

the three-dimensional structures of proteins are defined by their amino acid sequences; or, the structure of a protein is programmed in its amino acid sequence.

For example, exact DNA replication relies upon complementary hydrogen bonding between nucleobases.

In programmed systems, the structural information in the units must be transferred precisely to the assembly.

Several artificial helicates are created similar to DNA helix.

The formation of shape-defined supermolecules requires direction-specific molecular interactions.

Hyrogen bonding - because hydrogen bonding requires a specific geometry for the pair of interacting components.

H- bonding is important interaction for precise recognition.

Supramolecular Assembly via Fuzzy Interactions

Supramolecular assemblies based on less precise recognition processes sometimes produce more flexible, sensitive and adaptable functionality.

Cell membranes, are best example of a natural supramolecular assembly based on fuzzy molecular interactions.

fuzzy (unclear or un-precise)

Other egs. are Micelles, Liposomes, Vesicles, cast films etc….

Simplified illustration of a cell membrane

The structure of the cell membrane comprises lipids that form a double-layer structure containing floating proteins.

Structures and Formation Mechanisms of Cell Membranes:

assembly of mainly lipids and proteins. (eg. lipid bilayer structure).

The structure of the cell membrane comprises lipids that form a double-layer structure containing floating proteins.

The major driving force for lipid bilayer formation is hydrophobic interaction.

A lipid molecule consists of a hydrophilic head and hydrophobic tail.

Conceptual structure of an amphiphile

Amphiphiles - Molecules that have affinities for both hydrophilic and hydrophobic media. Eg. Lipids

many kinds of artificial amphiphiles are reported to form membrane-like structures in aqueous media.

When amphiphilic molecules are dispersed in water, the polar part of the amphiphile tends to expose itself to bulk water while the hydrophobic part shields itself from the aqueous phase, forming an assembly through hydrophobic interactions.

Micelles –Dynamic Supramolecular Assemblies

The simplest kind of supramolecular assembly formed by amphiphiles is the micelle

surfactants or detergents.

Such molecules show relatively high solubility and easily disperse in water up to a certain concentration level, above which they form micelles.

This concentration is called the critical micelle concentration (CMC).

Liposomes, Vesicles and Cast Films – Supramolecular Assemblies Based on Lipid Bilayers

Amphiphilic molecules or lipid molecules sometimes form double-layer structures.

This structure is called a bilayer structure, and it can be used to model a cell membrane.

Liposome-like structures formed from various kinds of amphiphiles are sometimes called “vesicles”, while the term “liposome” is sometimes limited to assemblies from phospholipids.

The lipid bilayer structure, the fundamental structural unit of liposomes and vesicles.

Liposomes are lipid bilayer structure extends two-dimensionally and forms the “skin” of a closed sphere that has a water pool inside.

This capsule-like structure can be thought of as a simplified model of a cell.

Liposome or vesicle with a lipid bilayer membrane

lipid bilayer behaves as a thermotropic liquid crystal

The gel (or crystalline) to liquid-crystalline transition

temperature at which the change in state occurs is called the gel (or crystalline)–liquid crystalline phase transition temperature.

Thin films of bilayer forming amphiphiles are called cast films, has a multilayered lipid bilayer structure.

It is prepared by gradual evaporating water from a solution of aqueous vesicles on a solid support.

Cast film with a multibilayer structure

The cast film has a structurally anisotropic nature.

It can provide an anisotropic medium for material syntheses.

Using cast film as a template, structurally anisotropic materials can be synthesized.

Formation of an anisotropic polymer in the interlayer spaces of lipid bilayers

Applications of Supermolecules

Supermolecules capable of electron conduction and electrical

switches (molecular electronic devices), supermolecules that

respond to light and manipulate photonic information

(molecular photonic devices), supermolecules that can be

used for information processing and calculations (molecular

computer), and supermolecules that move, rotate, and catch

targets (molecular machines) are introduced as examples of

molecular devices.

Molecular Device is the development of ultra small functional systems is predicted to enhance our standard of living.

Scanning Probe Instruments

Scanning Tunneling Microscope (STM)

Atomic Force Microscope (AFM),

These type instruments are Scanning Probe Instruments.

These microscopes have a nanoscale probe tip, or stylus, which slides along the sample surface and scans it. In the functioning of STM the amount of electrical current flowing between scanning tip and surface of particles. In the case of AFM, the force exerted on the nanoprobe as it moves along the surface is measured electronically.

MicroscopesOptical MicroscopeScanning Electron MicroscopeTransmission Electron MicroscopeScanning Tunneling Microscope

Heinrich Rohrer and Gerd Binnig

The Nobel Prize in Physics 1986Scanning Tunneling Microscope

Surface of Nickel.

Fe atoms on a Cu surface

STM

These examples suggest that supramolecular chemistry will be the main tool used in the development of nanotechnology – technology based on devices with nanoscale features – which is predicted to revolutionize our lives in the near future.

Nano Machines

Molecular Machines

Binding of ion A to the host induces the binding of ion B

Supramolecular chemistry - ApplicationsPhase transfer agents

Drug delivery

Separation of mixtures

Molecular sensors

Swithces and molecular machinery

Catalysts


Drug deliverySeparation of mixtures

Molecular sensors

Swithces and molecular machinery

Catalysts


Supramolecular chemistry - Applications

Phase transfer agents

Drug delivery


Molecular sensorsSwithces and molecular machinery

Catalysts


Phase transfer agents

Drug delivery


Molecular sensors

Swithces and molecular machineryCatalysts



Drug delivery


Molecular sensors

molecular Swithces and

Catalysts

Supramolecular photochemistry

Photochemistry is the branch of chemistry concerned mainly with the chemical effect induced by radiations lying in the UV and visible region .

Scheme for photochemical supramoleculeThe important parts are..

I. receptorII. SpacerIII. Signaling unit IV. substrate

Crown- anthracene system- a fluorescent sensor

systemi) Receptor (Host) : crown ether,ii) Substrate (Guest) : K+, iii) Signalling unit : anthracene iv) Spacer : –CH2-.

Supramolecular devicesThese are molecules or assemblies that

can perform functions such as linear or rotational movement, switching and entrapment. These devices exist at the boundary between Supramolecular chemistry and nanotechnology and prototypes have been demonstrated using Supramolecular concept.

Mainly they are classified in to

1) Molecular photonic devices : In these molecular recognition can be used to control light emission from molecules. These are photoactive supramolecules.

2) Molecular electronic devices : These includes molecular wires and switches.

Dimer naphthalene formation results in stronger emission

Inclusion of a guest inside the cavity of a cyclodextrin induces light emission

Light emission upon the binding of a potassium ion to a crown ether

(Photon-induced Electron Transfer).

1) Molecular photonic devices :

2) Molecular electronic devices :

These includes molecular wires and switches.

Molecular wires

Molecular wire in a lipid bilayer

electron flow across the bilayer membrane.

SWITCHING DEVICES

Electrical switch is used for regulating electron flow (current). Certain supramolecules mimics this electric switch are known as Molecular Switches.

There are mainly two kinds of molecular switches,

1) photoregulated molecular switch

2) chemically controlled molecular switch.

Photoregulated molecular switches

cis (on) trans (off)

a photosensitive azobenzene part at its center with crown ethers on both sides.

Photo-induced Molecular switch causing guest binding

Other eg for photo-induced switch is Molecular Rectifier. A rectifier is a device that allows only one way flow of electrons.

The switching ability is highly reversible by alternating irradiation by UV and visible light.

OFF ON

mimics an electrical switch. When it is cyclized, a fully conjugated path through the molecule becomes available, and is turned ON.

Chemically controlled molecular switch

disulfide formation decreases guest binding ability because it blocks guest insertion

Since the thiol groups only exist inside the cavity, intermolecular disulfide formation is also suppressed

Electron driven (chemically controlled) Molecular switch

OO

O

OSS

O

O

OO

O

OO

O

SH SH

r e d u c t io n

o x id a t io n

ON (I) (II) OFF

Compound I can bind ions but (II) can not. i.e. (I) on reduction loses the binding property.

These interconversion, ie. OF-ON mechanism is done by reduction and oxidation of these compounds.

chemically controlled Molecular switch

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Supramolecular chemistry