Supramolecular Chemistry
NTN-603
Metalloproteins
Structure of Heme and Hemoglobin (Hb)
Hb
Structure of Heme
4 x Heme group + 4 x Polypeptide chain
3
3
3
Supramolecular Chemistry
3
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Supramolecular Chemistry
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O2 Binding in Hemoglobin
Supramolecular Chemistry
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Structural Variation of Hb during O2 Binding(Latest Approach)
DeoxyHb
OxyHb
Fe(II) (0.78 Å), 5 coordinate
Fe(III), 6 coordinate
Domed, Nonplanar
Planar, O2− ion
0.6 Å above the ring
Fit into the ring
High Spin, Paramagnetic
Low Spin,
Diamagnetic
Supramolecular Chemistry
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Hb or Mb during O2 Binding
(O2 acts as π-Acceptor ligand)
Supramolecular Chemistry
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Perutz Mechanism
•Very fast
1.
Fe(II) in T state site above heme
Fe(II) binds to O2
Fe(II) pulled down into heme (R state)
2.
Fe(II) pulls down His F8
F helix tilts
Animation
Supramolecular Chemistry
NTN-603
Perutz Mechanism
3.
4.
•
•
Shift of tertiary structure causes shift of quaternary structure (rotate)
a2b1 and a1b2 interface residues realign
C-terminal residues break ionic interactions which stabilize T state
As R state forms from T state, it adopts ideal conformation for next O2
binding
All binding sites are altered, not just the one binding the O2
Supramolecular Chemistry
NTN-603
Perutz Mechanism: Pictorial
Representation
Supramolecular Chemistry
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DEOXYGENATED VS. OXYGENATED
HEMOGLOBIN (CONT.)
• The transition of hemoglobin from the T- to the R-state is not well-defined
• Best explained as a combination of a sequential and a concerted model
• It is unknown whether the a and b subunits differ in O2 affinity and which
subunit binds to (or releases) O2 first.
Supramolecular Chemistry
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Bohr Effect
•Conformational change will be
accompanied by change in IF’s
–Change in charge
•Also, H+ and O2 compete for
binding to Hb
•Relate pH to affinity
–Bohr effect
–O2 affinity increases as pH
increases
–Animation (YO2 = q)
Supramolecular Chemistry
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Carboxy Peptidase
Supramolecular Chemistry
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Mechanism of Carboxy Peptidase
Supramolecular Chemistry
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• The Carboxyl oxygen of the peptide bond
to be cleaved is ccordinated with the zinc
ion
1 The tyrosine side chain of the substrate binds to the
non-polar pocket in the active site of the enzyme.
2 The NH-hydrogen of the peptide bond to be cleaved is
hydrogen bonded to the OH group of tyrosine 248.
3 The negatively charged terminal carboxylic group of
glycyltyrosine (substrate) interacts electrostatically with
the positively charged side chain of arginine 145.
4 The carboxyl oxygen of the peptide bond to be cleaved
is coordinated to the zinc ion.
5 The terminal amino group of the peptide chain is
hydrogen bonded through the water molecule to the
side chain of glutamate 270.
Supramolecular Chemistry
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Two aspects of catalytic mechanism will be
discussed for carboxypeptidase A:
• Induced Fit:
The binding of
substrate is
accompanied by quite
large alteration in the
structure of the active
site.
Supramolecular Chemistry
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• Electronic strain:
The enzyme contains Zinc atom and other
groups at the active site that induce
electronic rearrangement of the substrate
to be more susceptible to hydrolysis.
Supramolecular Chemistry
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• Zinc is located in a
groove
near
the
surface
of
the
molecule cordinated
in a tetrahedral array
of two histidine side
chain, a glutamate
side chain and a
water molecule.
Supramolecular Chemistry
NTN-603
Nonplanar Perhaloporphyrins as Anion Sensors
H2TPP(NO2)Cl7 (1)
H2TPPCl8 (2)
Side View of 1
Side View of 2
Por
B bands (nm)
Q Bands, nm
λem, nm
1
363(26.91), 461(190.5)
559(10.23), 612(9.54), 730(7.58)
809
2
356(24.54), 455(204.1)
552(11.48), 601(11.75), 718(6.17)
762
3
371(33.85), 473(239.9)
574(9.55), 628(13.49), 747(9.12)
816
4
364(31.62), 469(257.0)
570(11.48), 623(16.98), 739(8.70)
789
The values in parentheses refer to ε×10-3 L mol−1 cm−1
Supramolecular Chemistry
NTN-603
Colorimetric Response and UV-Vis Spectral Changes
of 1 with tested Anions, Acid and Base
Supramolecular Chemistry
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Association Constants Data of Porphyrins with
Anions and their Detection Limits
CNlogβ2
nb
logβ2
nb
logβ2
nb
H2PO4logβ2
nb
1
10.57
2.2
10.53
2.7
9.59
2
9.39
2
2
3
9.56
11.36
2.0
2.4
9.33
11.12
2.3
2.8
8.77
10.21
2
2
8.68
9.86
2
2
4
10.23
2.1
8.76
2.3
8.95
2
8.72
2
Por
F-
OAc-
n refers to Hill coefficient, β2 as the association constant, r2 refers to correlation coefficient.
Por
F˗
CN-
CH3COO˗
H2PO4˗
LOD
nM (ppb)
LOQ nM
(ppb)
LOD
nM (ppb)
LOQ
nM (ppb)
LOD
nM(ppb)
LOQ
nM (ppb)
LOD
nM (ppb)
LOQ
nM (ppb)
1
7.3(0.19)
22.3(0.87)
6.0(0.11)
18.2(0.34)
8.2(0.48)
24.7(1.45)
7.7(0.75)
23.4(2.26)
2
9.5(0.24)
28.7(0.75)
8.4(0.16)
25.4(0.48)
9.7(0.57)
29.4(1.73)
9.6(0.93)
29.2(2.83)
3
8.6(0.22)
26.1(0.68)
7.4(0.14)
22.3(0.42)
10.0(0.59)
30.3(1.78)
10.3(1.00)
31.3(3.04)
4
8.3(0.21)
25.3(0.66)
8.4(0.16)
25.3(0.48)
8.7(0.51)
26.2(1.55)
8.6(0.83)
26.0(2.52)
The higher logβ2 values for H2TPP(NO2)Br7 (3) with all anions ascribed to enhanced nonplanar
conformation and electron deficient porphyrin core due to nitro and bromo substituents.
The general trend in β2 values for free-base porphyrins and anions were found to be 3 > 1 > 4 >2
and CN‒ > F‒ > CH3COO‒ > H2PO4‒ respectively.
Supramolecular Chemistry
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Plausible Mechanism for Anion sensing,
Protonation and Deprotonation
RR
X
X
X
X
+
NH
NH
X
X
H+N
TFA/Toluene
NH N
+
H N
NH+HN
X
X
X
X
X
X
N
N
-
N
X
X
X
R= NO2, X= Cl, 1
R= Cl, X= Cl, 2
R= NO2, X= Br, 3
R= Br, X= Br, 4
X
X
X
X
X
N
TBAOH/Toluene
N HN
X
X
Reversibility & Reusability Studies
X
X
X
R
X
R
X
X
TBAX/ Toluene
TBA(A)/
Toluene
X= CN
, F-,3COO
OAc--,H
(A)=
F , CH
, H2PO
2PO44
HA
R
X
X
N
N
X
N
-
N
X
X
X
X
HA
Supramolecular Chemistry
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‘Naked-eye’ Selective Detection of CN‒ ions
using Ni(II) Porphyrins
Objectives of This work
Por
Redox Potentials (V)
1st Ox
1st Red
1
1.48
-0.39
2
1.40
-0.42
3
1.33
-0.42
4
1.34
-0.63
5
1.28
-0.81
NiTPP
1.00
-1.32
❖ Synthesis of β-Substituted Ni(II) Porphyrinsin order to tune the Electronic
Spectral and Electrochemical Redox Properties.
❖ To Explore the Anion Detection Properties of these Macrocycles.
Supramolecular Chemistry
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‘Naked-eye’ CN− ion Sensing using Ni(II) Porphyrins
UV-Vis spectral titration of 1 upon addition
of TABCN
UV-Vis spectral features of 1 with various
anions in toluene at 298 K
1
1+
2CN-
Binding Constant Data of 1-5 with CN− ions and their Detection Limits in Toluene
Porphyrin
1
2
3
4
5
β2
3.86×1016
1.95×1016
6.70×1012
1.21×109
7.79×108
r2
0.90
0.92
0.90
0.99
0.97
n
3.33
3.33
2.68
2
2
LOD (ppm)
0.108
0.108
0.104
0.062
0.103
m
2
2
2
2
2
aWithin the error of ±0.04; n = Hill coefficient; LOD = Limit of detection; m = Stoichiometry
Supramolecular Chemistry
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Ratiometric Sensing and Cooperative Behaviour
Ratiometric response towards
CN− ions in presence of other anions
Positive Cooperative behaviour
of 1-3 with cyanide ion
❖ Competition experiments demonstrates the tolerance of 1 towards
potentially interfering anions and selectively detects CN− ion.
❖ Higher Hill coefficients and sigmoidal curves reflects the positive cooperativityin cyanide ion binding.
Supramolecular Chemistry
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DPV Changes of Ni(II) Porphyrins upon addition
of 2 equivalents of CN‒ions in CH2Cl2 at 298 K
Por
1•2CN‒
1
Porphyrin (without CN‒)
Porphyrin2CN−
1st Ox
1st Red
1st Ox
1st Red
1
1480
-392
1132
-552
2
1400
-416
1135
-675
3
1332
-420
1000
-612
4
1340
-630
820
-860
5
1280
-810
783
-1102
Cathodic shift both in first oxidation and reduction as expected upon
addition of cyanide ion.
Supramolecular Chemistry
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Reversibility and Reusability Test
❖ Recovered 1 was again treated with of CN‒ ions which shows similar spectral
features as that of fresh solution of 1 and thus confirms reusability.
Supramolecular Chemistry
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Practical Application of Porphyrin Sensors
as Test Trips
Toluene solution
Aqueous solution
Toluene solution
Aqueous solution
Supramolecular Chemistry
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Crystal Structure of 3•CN− and Optimized Geometry
of 1•2CN−
Top view
Top view
Schematic Representation of Cyanide ion Binding
Porphyrins are able to detect as low as ~0.11 ppm solution of CN− ions
Supramolecular Chemistry
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β-Dicyanovinyl appended Porphyrin
Chemodosimeters
Single Crystal X-ray Structure of NiTPP-MN
Characterization: UV-Vis, FL &1H NMR spectroscopic techniques, Mass spectrometry, EA and Single crystal XRD
Supramolecular Chemistry
NTN-603
‘Naked-eye’ Selective Detection of CN‒ ions
UV-Vis Absorption Spectra in Toluene
Colorimetric Cyanide Sensing
Supramolecular Chemistry
UV-Vis Spectral titration of 1 with CN−
Applications
NTN-603
Ratiometric Cyanide Sensing
CVs of 1 and 1+CN− in CH2Cl2 at 298 K
1H NMR Spectra of 1 and 1+CN− in CDCl
3
Proposed Mechanism for CN− Sensing
These porphyrins exhibited LOD of 0.023-0.082 ppm
Supramolecular Chemistry
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Molecular Structures of β-Functionalized Porphyrins
R
N
R'
N
N
M
N
N
N
N
X
N
M
M
N
N
NO2
N
N
N
M
N
N
N
Br
Br
"R
"R
R = CHO, M = Ni(II) (1), Cu(II)
(1a), 2H (1b);
R' = CHO, M = Ni(II) (5), Cu(II)
(5a), 2H (5b);
R" = CHO, M = Ni(II) (9),
Cu(II) (9a), 2H (9b);
X = CHO, M = Ni(II) (11),
Cu(II) (11a), 2H (11b);
R = CH=C(CN)2, M = Ni(II) (2),
Cu(II) (2a), 2H (2b);
R' = CH=C(CN)2, M = Ni(II) (6),
Cu(II) (6a), 2H (6b);
R" =CH=C(CN)2, M = Ni(II)
(10), Cu(II) (10a), 2H (10b);
X =CH=C(CN)2, M = Ni(II)
(12), Cu(II) (12a), 2H (12b);
R = CH=C(CN)(COOC2H5), M =
Ni(II) (3), Cu(II) (3a), 2H (3b);
R' = CH=C(CN)(COOC2H5), M =
Ni(II) (7), Cu(II) (7a), 2H (7b);
R = CH=C(CN)(COOH), M = Ni(II)
(4), Cu(II) (4a), 2H (4b)
R = CH=C(CN)(COOH), M =
Ni(II) (8), Cu(II) (8a), 2H (8b)
These porphyrins were characterized by various spectroscopic techniques and single crystal XRD analyses.
Supramolecular Chemistry
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Chemodosimeters
ual-Colorimetric changes by addition of various anions to NiTPP-ECA (3), NiTPP(Br)2-MN (
NiTPP(Br)2-ECA (7), NiOPP-MN (12) and NiTPP-CAA (4)
NiOPP (12)
CN−
Cl-
Br-
H2PO4-
F− CH3COO− Cl−
F-
CN-
HSO4-
I-
H2PO4−
I−
HSO4−
PF6−
OAc-
ClO4−
ClO4-
PF6-
NO3− Br−
4
NO3-
Chemosensor
Supramolecular Chemistry
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Mode of Interaction: Chemodosimeter vs Chemosensor
Chemodosimeter but spectroscopically
silent
Chemodosimeter
Chemosensor
Chemodosimeter
Supramolecular Chemistry
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‘Lab-on-a-molecule’ Approach for Discrimination of
Toxic F‒ and CN‒ ions
Molecular Structure of MTDtBuHPP-MN
Crystal Structure of CuTDtBuHPP-CHO
(a)
CN– ion responsive moiety
F– ion responsive
moiety
(b)
UV-Vis Spectra and CVs of CuTDtBuHPP-CHO/MN in CH2Cl2 at 298 K
Supramolecular Chemistry
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Switching between Porphyrin, Porphyrinogen and
Anionic Porphyrin in presence of F− and CN− ions
Supramolecular Chemistry
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Switching between Porphyrin, Porphyrinogen and
Anionic Porphyrin in presence of F− and CN− ions
Supramolecular Chemistry
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Writing and Erasing Memory Cycles of Free Base
Porphyrins in Presence of CN‒ and F‒ ions
Supramolecular Chemistry
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UV-Vis Spectral Features of OxP-MN and OxP in CH2Cl2
UV-Vis Absorption Spectra of OxP-MN and OxP
OxP-MN has an absorption spectrum identical to OxP with marginal blue shift in absorption maximum
(Δλmax = 4 nm) leading to the observation that olefin-bridged electronic acceptor on the β-pyrrole carbon in
case of porphyrinogen resulted in only abated shift in spectrum in contrast to its porphyrin analogue.
Supramolecular Chemistry
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Response of OxP-MN towards Picric Acid (PA)
picric acid (PA)
OxP-MN, all nitroaromatics
Picric Acid
Neutral Species
Supramolecular Chemistry
OxPH22+•2PA−
NTN-603
Reusability and Practical Applicability
Supramolecular Chemistry
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Absorption Spectral Features of OxP-MN on Sequential
Addition of PA and F– ions
Titration of OxP-MN with PA following F–
path A
path B
Titration of OxP-MN with F– following PA
path C
Picrate ion
PA to Picrate ion
path A’
path B
path A’
path B’
path C’
path B’
path A
path C
Supramolecular Chemistry
path C’
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Mechanism of Unrestricted Indicator Displacement (IDA)
Assay Pathway using PA and F–
Supramolecular Chemistry
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Mechanism of Unrestricted Indicator Displacement
Assay Pathway using PA and CN–
Supramolecular Chemistry
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UV-Vis Spectral Changes of OxP-MN and
OxP in presence of F‒ and CN‒ ions
423 nm
434 nm
464 nm
636 nm
649 nm
Supramolecular Chemistry
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Schematic Representation of Protection-Deprotection
Statergy for Boronic Esters
Supramolecular Chemistry
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Schematic Representation of ProtectionDeprotection Statergy for Boronic Esters
Colorimetric Detection of Anions
1a
F¯
H2PO4¯
CN¯
H2O
Supramolecular Chemistry
NPG
Electronic Spectral Data of 1a in presence of Anions
Porphyrin
λabsorption(nm)
λemission(nm)
1a
1a + H2PO4‒
1a + F‒
1a + CN‒
420, 548, 586
428, 566, 606
433, 567, 610
441, 582, 625
601, 648
609, 646
624, 657(sh)
634, 690(sh)
NTN-603
Tunable Two-input/Multi-output System for Free Base
Porphyrin using CN‒ and F‒ ions as inputs
Memory element
λabs.
426 nm
λabs.
464 nm
λabs.
638 nm
λem.
749 nm
λem.
710 nm
INPUT
= CN—
INPUT
= F—
0
0
“0”
“1”
“0”
“1”
“0”
1
0
“0”
“0”
“1”
“0”
“1”
0
1
“1”
“0”
“0”
“0”
“0”
1
1
“0”
“0”
“1”
“0”
“0”
---------------------------------------------------------------------------------------------------------------------
Supramolecular Chemistry
NTN-603
Detection of Toxic Ions and Picric Acid using Organic Sensors
OH
O2N
FRET
NO2
O2N
NO2
HO
N
N
NH2
HO
N
N
N H
H
O
H
NO2
O2N
enap-OH (1)
Supramolecular Chemistry
nap-OH (1)•PA
NTN-603
Molecular Device Preparation using
Supramolecular Systems
Supramolecular Chemistry
NTN-603
Various Devices using Supramolecular Systems
Supramolecular Chemistry
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Characterization of Molecular Systems to
Self-assembled Supramolecular System
Scanning Probe Microscopy (SPM) is useful to study about Surface Topography
Supramolecular Chemistry
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Electron Transfer through Conjugated Molecules
Electron conducting wire
The length of this molecular wire fits the width of a phospholipid bilayer, and the wire
is accommodated effectively into the bilayer skin of a liposome for electron transfer.
Supramolecular Chemistry
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Molecular Photonic Switch
Azobipyridine acceptor
Azobipyridine is an acceptor in its neutral state, If it is reduced the electron accepting
character decreases. Under such situation, energy transfer takes place from Ru(II) to
Os(II).
Supramolecular Chemistry
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Energy Transfer Device with a Photoswitching Device
Excited thiacyanine molecules in the donor layer can transfer energy via the merocyanine
to the indocarbocyanine in the acceptor layer. This results in strong indocarbocyanine
fluorescence at 725 nm (λ2). On the other hand, irradiating the system with visible light
changes the switching layer into its spiropyran form, which cannot accept energy from
thiocyanine.
Supramolecular Chemistry
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An Artificial Molecular Machine that builds an Asymmetric
Catalyst
David A. Leigh et al, Nature Nanotechnology | VOL 13 | MAY 2018 | 381–385
An artificial
molecular
machine that
builds an
asymmetric
catalyst
Supramolecular Chemistry
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Various Molecular Containers for Host-Guest Chemistry
Rafel et al,
Nature Nanotechnology
| VOL 15 | April 2020 |
256–271 |
Supramolecular Chemistry
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Electrically Conducting Self-assembled Nanomaterials
Through Supramolecular Interactions
Nicolas et al, Nanoscale, 2013, 5, 7098–7140
Supramolecular Chemistry
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Supramolecular Chemistry
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Monolayer at Air-Water Interface
Supramolecular Chemistry
NTN-603
Amphiphile Aggregates
Supramolecular Chemistry
NTN-603
Self-assembled Monolayer at Gold Surface
Supramolecular Chemistry
NTN-603
SWCNT and KI Incorporation in it
Supramolecular Chemistry
NTN-603
Dendrimer – Supramolecular Interactions
Divergent Synthetic Approach
Supramolecular Chemistry
NTN-603
How does Gecko stick to the walls?
Supramolecular Chemistry
NTN-603
MWCNTs and Their Surface Etching
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Spectroscopic Methods to Study
Supramolecular Interactions
Supramolecular Chemistry
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Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
NTN-603
Supramolecular Chemistry
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Supramolecular Chemistry
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Supramolecular Chemistry
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Supramolecular Chemistry
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Supramolecular Chemistry
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The End
&
All the best
Supramolecular Chemistry
NTN-603