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Corso CFMA. LS-SIMat 1
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Chimica Fisica dei Materiali AvanzatiChimica Fisica dei Materiali Avanzati
Part 2 – Supramolecular chemistry and molecular Part 2 – Supramolecular chemistry and molecular recognitionrecognition
Laurea specialistica in Scienza e Ingegneria dei MaterialiCurriculum Scienza dei Materiali
Corso CFMA. LS-SIMat 2
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Supramolecular chemistrySupramolecular chemistry ...can be defined as the ““chemistry beyond the moleculechemistry 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
Cellinterior
Cellexterior
O
OH
NH+
O
O_
+
E
A
D
B
C FG
Bacteriorhodopsin
K+
K+
K+
Cellinterior
Cellexterior
Ion channels ATP Synthase
Corso CFMA. LS-SIMat 3
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Supramolecular chemistry - 2Supramolecular 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
O OO
OO
OO
O
OO
O
OOO
O
O
O
OO O
O O
O
O
OO
O
O
OO
OO
O
O
O
OOO
OO
O
O
OO
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
OO
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
OOO
OO
OO
O
OO
O
O OO
O
O
O
O
MIII
N
N
NN
NN
N
N
N
N
OO
O
O
O
OO
OO
O
O
O
+
+
+
+
6+
RuII
Rotaxane
Dendrimeric structure
Corso CFMA. LS-SIMat 4
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Coordination bondingCoordination 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)
N
NH N
HN
N
N
NN
NN
N
N
ZnN
NN
N
N
N
Zn
RuIIOC CO
Cl
Cl
RuIIOC CO
Cl
Cl
N
NH N
HN
N
NNN
NN
N
N
ZnN
NN
N
N
N
Zn
RuIIOC CO
Cl
Cl
RuIIOC CO
Cl
Cl
Corso CFMA. LS-SIMat 5
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Molecular recognitionMolecular 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 receptorSelective binding of a substrate by a receptor
Interaction =
ENERGYENERGY
Selection =
INFORMATIONINFORMATION
receptor and substrate should exhibit Steric complementarity (shape and size) Interactional complementarity Large contact areas Multiple interaction sites Strong overall binding
Corso CFMA. LS-SIMat 6
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
At the origin of molecular recognitionAt 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
Binding of Ritonavir inhibitor to a protease
Active site
Corso CFMA. LS-SIMat 7
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Spherical recognitionSpherical recognition Recognition of metal cations
Spherical guests: metal cations (Na+, Ca2+, La3+) and halide anions (Cl-, I-, etc.)
R
O O
R
O
O
O
O
Ca2+O O O O O O RR
Ca2++
Charles Pedersen, 1967
Crown Crown EthersEthers
Corso CFMA. LS-SIMat 8
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
RotaxanesRotaxanes
A case of ingenious use of [NHO] and [NCHO] H-bonds between di-alchil-ammonium cations and crown ethers
J. Fraser Stoddart et al. (UCLA)
Corso CFMA. LS-SIMat 9
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Rotaxanes as molecular machinesRotaxanes as molecular machines
Shuttling action by cemical chemical stimulation
Corso CFMA. LS-SIMat 10
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
CatenanesCatenanes
With the same interactions it is possible to obtain a different type of interlaced structure: the catenanes
Proposed mechanism:1. Formation of a tri-cationi
intermediate
2. Formation of a charge transfer complex
3. Self-assembly promotes the interlaced structure
4. The catenane is afforded (in a 70% yield)
Corso CFMA. LS-SIMat 11
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Molecular recognition portfolio: cavitandsMolecular recognition portfolio: cavitands
Corso CFMA. LS-SIMat 12
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Anatomy of cyclodextrinsAnatomy of cyclodextrins
Corso CFMA. LS-SIMat 13
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Bonding by hydrophobic effectBonding by 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.
Solvated host Solvated guest Complex
The hydrophobic effect
Corso CFMA. LS-SIMat 14
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
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 effect (cont’d)
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: 2
2
mJ/m 5040 tensionlinterfacia
mJ/m 3015 tensionsurface
E
E
Corso CFMA. LS-SIMat 15
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
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.
Advantages:Because 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.
Application: Molecular-recognition-based SensorsApplication: Molecular-recognition-based Sensors
Corso CFMA. LS-SIMat 16
UUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVAUUNIVERSITA’ DEGLI NIVERSITA’ DEGLI SSTUDI DI TUDI DI PPADOVAADOVA
Application: Molecular-recognition-based Sensors Application: Molecular-recognition-based Sensors - 2- 2
WAVEGUIDE BASED OPTICAL CHEMICAL SENSOR
AbstractThe 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.
