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