Molecular Sensor - 國立臺灣大學mkleung/course/orgmaterial...Pattern Recognition (1)...
Transcript of Molecular Sensor - 國立臺灣大學mkleung/course/orgmaterial...Pattern Recognition (1)...
Molecular Sensor
Basic Structure about a chemical sensor
Binding Site Signaling System (optical or Electrochemical)
Binding of the target molecule
(i) Selectivity: Molecular Recognition. Key and Lock Model(ii) Revisibility(iii) Forces for binding (medium Strength)
Coordination ComplexationHydrogen bondPi-pi interactionHydrophobic Interaction
N Fe Ligand to Metal Coordination 10-30 Kcal/mol
N H O Hydrogen Bond 3 - 5 Kcal/mol
van der Waals Force Less than 1 kcal/mol
π-π Stacking
The kinetically labile bonding between the constituents contribute to relatively defect free, self healing assemblies of high structural integrity, as a result of the equilibrium between constituents and final products.
e.g.–OH…O 3300 cm-1 ; –OH 3600 cm-1 ∆νs=-300/3300 = -10%
Strong Hydrogen Bonds
Donor:
O H N H
Acceptor
N F, OH, OR, O-P
Ionic Hydrogen Bonds; Gas-Phase Dimers
,
Moderate Hydrogen Bond:
Generated by Neutral Bonor and Acceptor Groups:
Donor
ROH, R2NH, RNH2
Acceptor
R2O, O=CR2, N(X-H) X:electronegative atom Lone pair
Weak Hydrogen Bonds:
Donor
Acceptor
C-H, Si-H
F-C F-S
C
H
Cl ClCl
Nature of Hydrogen Bonds
The hydrogen bonding occurs in the direction of the conventionally viewed lone pairs of the acceptor
O
HX
O
HX
HX
More stable than O HX
Special Cases
O
HX
HX
HXO
O HX
XH
HX
XH
Stronger the Acceptor, Shorter the Distance, and Stronger Directional Effect
Hydrogen bond for anion is proportional to their basicity
X-H…Y- X … H-Y-
PO43- > RCO2
- > ClO4- > and F- > Cl-
Solvent Dependent Proton Transfer Process
O
OHH
NH
HHO
OHH
NH
HH
ε = 1
40 kJ/mol more stable
200 kJ/mol less stable
than the separated species
But in ε = 4, Acid-Base is more Stable
Cooperativity of Hydrogen bonding Interactions
(1) Hydrogen Bonding Assisted Resonance
Gilli, 1989
X-RayDue to resonance effectd1, d3 are shortenedd2, d4 are lengthened
Hydrogen Bonding Assisted Resonance
NO
O
H
Unusually Strong
NO O
O
HO
Intermolecular Hydrogen Bonding Assisted Resonance
Increased by 0.018A
Decrease by 0.023A
Chain Type Structures
DNA Base-pair
Pattern Recognition
(1) Combination; (2) Orientation
Using the association data currently available in literature, a hydrogen bond in solution can be expected to furnish a contribution in ∆G not greater that 20-30 kJ/mol.
Arrays of the HB donors and acceptors, are there any different in stabilization energy?
Two units: D......AD......A
D......AA......D
Three Units D......AD......AD......A
D......AA......DD......A
D......AD......AA......D
Four Units D......AD......AD......AD......A
D......AD......AD......AA......D
D......AD......AA......DA......D
D......AA......DD......AA......D
A......DD......AD......AA......D
D-H.....A or D.....A p = 7.9 kJ/mol
2p+2s 2p-2s p = 7.9 kJ/mol or 1.88 kcal/mols = 2.9 kJ/mol or 0.69 kCal/mol(-) for repulsive; (+) for attractive
3p+4s 3p3p-4s
Examples
N
N
N
N O
O
R
HN
N
N
O
O
Et
Et
H
H
A
D
A
D
A
DFlavin
N
N
NN
O
H
N HH
NN
N
O R
HHA
D
D
D
A
A
Guanine Cytosine
Examples for binding
N N NPh Ph
N NNH H H
H H
OO
OPrOPr H Ar
Ka > 105
∆G > 7 kcal/mol
N N NPh Ph
N NNH H H
H H
Ka > 70
∆G = 2.5 kcal/mol
O
OEt
N N N
O
Br
CH3
H
N O
Pf
Ar
NH
H H
Ka > 1.7x104
∆G = 5.8 kcal/mol
Preorganization Effect
DD A
A
D
D
A
A
D
D
A
A
D
D
A
A
Entropy loss: ∆S(intra) + ∆S (Inter)
Entropy loss: ∆S (Inter)
N
NN N
N
N
CN CNN N
H H
HH
O
N NH H
H H
Ks=1.4x104
Molecular Lego
Lamellar ceiling
Structural pillars
Guest-filled pores
Lamellar floor
Lamellar ceiling
Structural pillars
Guest-filled pores
Lamellar floor
90o180o
120o
109.5o
180o
120o
90o
90o
60o
One Dimensional Motif
Cyclic Motif
Figure 4. Schematic representation of the interconversion of two helical monomers and a double helical dimer. This corresponds to a spring-like compression/extension of the monomers.
Figure 7. Crystal structure of the double helicaldimer of the heptameric strand 2. In the stick representations, CH hydrogens are ommitted for clarity. Dashed lines indicate intermolecular hydrogen bonds between the strands, or between one strand and co-crystallized water or nitrobenzene molecules. Other co-crystallized solvent molecules are not represented. a) Stick representation of a right-handed double helix. The two strands are coded in different colors; b) CPK representation of a different view of the right handed double helix. The two strands are almost super-imposable upon a 1808 rotation about the helix axis. c) Stick representation of a neighboring pair of right- and left-handed double helices. In this view, the pinching of the duplex at one end, and its opening at the other end are clearly visible.
Arrays through Hydrogen-Bonding Interactions
Molecular Recognition
The Heart of a Sensor
Design of a binding site: A combination of Electrostatic force, Hydrogen bond, πstacking and Molecular Geometry
Binding of Ammonium Cations by Corands
Central and Lateral DiscriminationPrimary >> Secondary, Tertiary amines
Binding of Guanidinium Ion
Ditopic Receptors
Selectivity for n=5, 7, 10For +NH3(CH2)nNH3
+
Chiral Recognition
Catalyst for Ethanolysis
R CHNH3
OO
NO2
R CHNH3
OHO
EtOH
20% in CH2Cl2
L-amino acid esters ethanolysed 102 to 103 faster than the S-amino acid
Design of the Molecular Host
R amino acid S/R HostMe2CHCH2-PhCH2-Me2CHCH2CH2-Me-
9.28.26.01.0
R/S host for competition
Carbohydrate Recognition
N
N
N
NH
N
RO
O
O
O
O
O
O
O
O
HOHO
HO
OH
O
H
Ka = 5600/M (H)Ka = 7300/M (OBu)
Prof. Inouye
Amphiphilic Receptors
Polar
Non-Polar
Anion Host
Host for Phosphates
Hydrogen Bond Array Recognition and Molecular Tweezer
Angle/Array
Chiral Core
Edge to Face and Stacking of Face to Face Complexes
The permanent negative charges of p-electron clouds will lead to repulsion in face-to-face complexes unless the aromatice units are so displaced that the correspondingly more positively charged aromatic hydrogen atoms can exert an attractive force towards the πsystem.
Stability: E-F > F-F by 3 kJ/mol
Face to Face Stacking
K = 290 M-1
Hydrogen Bond/π Interactions
K = 1.5 x 104 M-1