Chimica Fisica dei Materiali Avanzati Part 2

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Chimica Fisica dei Materiali AvanzatiPart 2
Supramolecular chemistry and molecular recognition

• Laurea specialistica in Scienza e Ingegneria dei
  Materiali
• Curriculum Scienza dei Materiali

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Supramolecular chemistry

• ...can be defined as the 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. (J.-M. Lehn)
• Molecular interactions form the basis of the
  highly specific recognition, reaction, transport,
  regulation, etc. processes that occur in biology

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Supramolecular chemistry - 2

• However, chemistry is not limited to systems
  similar to those found in biology but is free to
  create unknown species and to invent novel
  processes

Rotaxane
Dendrimeric structure
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Coordination bonding

• The scope of coordination chemistry extends to
  the binding of all kinds of substrates cationic,
  anionic and neutral molecular species of either
  organic, inorganic, or biological nature (J.-M.
  Lehn)

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Molecular recognition

• Molecular recognition is defined by the energy
  and the information involved in the binding and
  selection of substrate(s) by a given receptor
• It implies the (molecular) storage and
  supramolecular read out of molecular information

Selective binding of a substrate by a receptor
Interaction ENERGY
Selection INFORMATION

• receptor and substrate should exhibit
• Steric complementarity (shape and size)
• Interactional complementarity
• Large contact areas
• Multiple interaction sites
• Strong overall binding

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At the origin of molecular recognition

• 1894 Emil Fischer presents the lock and key
  model for enzymatic chemistry ?
• Molecular recognition
• Supramolecular function

Structure of glutamine synthetase a
homo-dodecamer
Active site
Binding of Ritonavir inhibitor to a protease
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Spherical recognition

• Recognition of metal cations
• Spherical guests metal cations (Na, Ca2, La3)
  and halide anions (Cl-, I-, etc.)

Crown Ethers
Charles Pedersen, 1967
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Rotaxanes

• A case of ingenious use of N?H?O and N?C?H?O
  H-bonds between di-alchil-ammonium cations and
  crown ethers

J. Fraser Stoddart et al. (UCLA)
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Rotaxanes as molecular machines

• Shuttling action by cemical chemical stimulation

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Catenanes
With the same interactions it is possible to
obtain a different type of interlaced structure
the catenanes

• Proposed mechanism
• Formation of a tri-cationi intermediate
• Formation of a charge transfer complex
• Self-assembly promotes the interlaced structure
• The catenane is afforded (in a 70 yield)

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Molecular recognition portfolio cavitands
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Anatomy of cyclodextrins
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Bonding by hydrophobic effect
Solvated host
Solvated guest
Complex
The hydrophobic effect

• Strong inclination of water molecules to form
  H-bonds with each other affects their interacn.
  with non-polar molecules not forming H-bonds
  (alkanes, hydrocarbons, fluorocarbons, etc.)
• Water molecules can pack around the non-polar
  solute without giving up any of their H-bonding
  sites (however, the size and shape of non-polar
  molecules is very critical)
• The net effect is a reorientation of the water
  molecules towards a structure more ordered that
  in the bulk liquid.

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The hydrophobic effect (contd)

• The increased order in the water cages is
  entropically unfavourable.
• For this reason, the hydrocarbons are very little
  soluble in water the free energy increases due
  to the decrease in entropy
• The free energy of solubilization is roughly
  proportional to the surface area of the molecules.

The hydrophobic interaction

• It arises primarily from the rearrangement of
  H-bond configurations in the overlapping
  solvation zone as two hydrophobic species come
  together.
• It is a cooperative effect of much longer range
  than any typical bond
• The hydrophobic interaction plays a central role
  in many surface phenomena, in molecular
  self-assembly, in micelle formation, in
  biological membrane structure and in determining
  the conformation of proteins.
• Example

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Application Molecular-recognition-based Sensors

• Technology need sensors which can distinguish
  extremely low level of gas species in the
  presence of large quantities of interfering
  species
• Required features sensitivity, selectivity,
  response time
• Proposed solution sensing chemicals by analysis
  of changes in the refractive index of a thin film
  of host reagent on a waveguide caused by the
  formation of guest-host inclusion complexes in
  the thin film.
• AdvantagesBecause the formation of inclusion
  complexes is reversible, the sensor apparatus can
  be used for substantially real-time sensing of
  chemical agents. Sensor sensitivity can be tuned
  and choice of chemicals to be detected can be
  made by varying the size of the host reagent
  cavities and by selecting the chemical
  functionality of the host reagent molecules.

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Application Molecular-recognition-based Sensors
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WAVEGUIDE BASED OPTICAL CHEMICAL SENSOR
Abstract The invention provides an apparatus and
method for highly selective and sensitive
chemical sensing. Two modes of laser light are
transmitted through a waveguide, refracted by a
thin film host reagent coating on the waveguide,
and analyzed in a phase sensitive detector for
changes in effective refractive index. Sensor
specificity is based on the particular species
selective thin films of host reagents which are
attached to the surface of the planar optical
waveguide. The thin film of host reagents
refracts laser light at different refractive
indices according to what species are forming
inclusion complexes with the host reagents.