Self-Assembly In Supramolecular
Chemistry
-- Inspiration From Nature
Reporter: Zhengming Tang
唐铮铭
Supervisor：Prof. Jian Pei
2006.11.3
1
Outline
Introduction
 Lessons from nature
 Scientists’ efforts
 Conclusion and outlook
 Acknowledgement

2
Outline
Introduction
 Lessons from nature
 Scientists’ efforts
 Conclusion and outlook
 Acknowledgement

3
Introduction
Nobel Prize in 1987: Pederson C , Cram D J, Lehn J M.
Supramolecular chemistry, a term introduced by JeanMarie Lehn, is “chemistry beyond the molecule”, that
is the chemistry of molecular assemblies using
noncovalent bonds.
Jean-Marie Lehn, Science 2002, 295, 2400
Freek J. M. Hoeben, E. W. Meijer, Chemical Reviews 2005, 105, 1491
4
Introduction
5
Freek J. M. Hoeben, E. W. Meijer, Chemical Reviews 2005, 105, 1491
Outline
Introduction
 Lessons from nature
 Scientists’ efforts
 Conclusion and outlook
 Acknowledgement

6
Lessons from nature
“The chemist finds illustration, inspiration, and stimulation
in natural processes, as well as confidence and
reassurance since they are proof that such highly complex
systems can indeed be achieved on the basis of molecular
components.”
Jean-Marie Lehn, 1995
Nature has evolved functional assemblies over millions of
years; hence, scientists often gather inspiration from the
beautiful structures that are encountered.
E. W. Meijer, 2005
7
Lessons from nature--AQP1
selective water permeation
Hydrophobic effects
8
Kazuyoshi Murata, Kaoru Mitsuoka, Teruhisa Hirai, Nature 2000, 407, 599-605.
Lessons from nature-light-harvesting protein PE545
Protein PE545 assembled with eight light-absorbing
molecules plays a key role in this photosynthetic system
Centre for Quantum Information and Quantum Control, University of Toronto,
Nature Materials 2006, 5, 683-696.
9
Lessons from nature-light-harvesting protein PE545
Centre for Quantum Information and Quantum Control, University of Toronto,
Nature Materials 2006, 5, 683-696.
10
Lessons from nature-DNA bound by base pairs
11
Outline
Introduction
 Lessons from nature
 Scientists’ efforts

Assembled by hydrogen bond
Assembled by п-п interaction
Assembled by metal-ligand
Scientists’ bionic results
Conclusion and outlook
 Acknowledgement

12
Outline
Introduction
 Lessons from nature
 Scientists’ efforts

Assembled by hydrogen bond
Assembled by п-п interaction
Assembled by metal-ligand
Scientists’ bionic results
Conclusion and outlook
 Acknowledgement

13
Scientists’ efforts
Assembled by hydrogen bond
First noted in 1892 by Nernst
Werner proposed his concept of “Nebenvalenz” (minor valence) in 1902
The theory that the hydrogen atom was the center of this weak interaction were
first made in 1920 by Huggins as well as Latimer and Rodebush.
Bernal and Huggins proposed the actual term “hydrogen bond” in 1935
“The discovery of the Hydrogen Bond could have won someone
the Nobel Prize, but it didn’t.”
George A. Jeffrey, Wolfram Saenger, 1991
14
The essence of hydrogen bond
1) Electrostatic or coulomb energy (Δ ECOU)
2) Exchange repulsion (ΔEEX)
3) Polarization energy (ΔEPOL)
4) Charge-transfer energy or covalent bonding (ΔECHT)
5) Dispersion forces (ΔEDIS).
15
Leonard J. Prins, Peter Timmerman, Angew. Chem. Int. Ed., 2001, 40, 2382-2426
The essence of hydrogen bond
16
Felix H. Beijer, E. W. Meijer, J. Am. Chem. Soc. 1998, 120, 6761-6769
Assembled by hydrogen bond
17
Takashi Kato, Norihiro Mizoshita, Angew. Chem. Int. Ed. , 2006, 45, 38– 68.
Assembled by hydrogen bond
18
Takashi Kato, Norihiro Mizoshita, Angew. Chem. Int. Ed. , 2006, 45, 38– 68.
Assembled by hydrogen bond
Design strategy
19
T. Yamaguchi, Takuzo Aida, J. Am. Chem. Soc. 2003, 125, 13934-13935
Assembled by hydrogen bond
TEM micrographs of (a,b) 1acid with C60
(c,d) 1acid alone.
T. Yamaguchi, Takuzo Aida, J. Am. Chem. Soc. 2003, 125, 13934-13935
20
Assembled by hydrogen bond
Left: Titration of 1acid (1.2 μM) with C70 ([C70]:[1acid] = 0:1–5:1)
Right: Titration of 1ester (1.2 μM) with C70 ([C70]:[1ester] = 0:1–6:1)
21
T. Yamaguchi, Takuzo Aida, J. Am. Chem. Soc. 2003, 125, 13934-13935
Assembled by hydrogen bond
Supramolecular peapods
22
T. Yamaguchi, Takuzo Aida, J. Am. Chem. Soc. 2003, 125, 13934-13935
Outline
Introduction
 Lessons from nature
 Scientists’ efforts

Assembled by hydrogen bond
Assembled by п-п interaction
Assembled by metal-ligand
Scientists’ bionic results
Conclusion and outlook
 Acknowledgement

23
Assembled by п-п interaction
Some simple models:
24
M. O. Sinnokrot, C. David Sherrill, J. Am. Chem. Soc. 2004, 126, 7690-7697
Assembled by п-п interaction
TEM photograph of an aggregate
of G3-T17-G3. n=5--6
Joke J. Apperloo, Rene A. J. Janssen, J. Am. Chem. Soc., 2001, 123, 6916-6924
Rene A. J. Janssen, Jean M. J. Frechet, Macromolecules, 2000, 33, 7038-7043
25
Assembled by п-п interaction
Absorption and emission spectra of (a)
molecularly dissolved (PL excited at 2.64
eV, solid lines) and aggregated (PL excited
at 2.20 eV, dashed lines) G3-T11-G3 in
dichloromethane and (b) molecularly
dissolved (PL excited at 2.61 eV, solid lines)
and aggregated (PL excited
at 2.11 eV, dashed lines) G3-T17-G3 in
dichloromethane.
Joke J. Apperloo, Rene A. J. Janssen, J. Am. Chem. Soc., 2001, 123, 6916-6924
Rene A. J. Janssen, Jean M. J. Frechet, Macromolecules, 2000, 33, 7038-7043
26
Assembled by п-п interaction
UV-vis (left) and fluorescence (right) spectra
of 2 in THF and butanol.
Blue shift: Δλ=50 nm for 1; Δλ= 71 nm for 2
Much lower fluorescence intensity
27
A. P. H. J. Schenning, E. W. Meijer, J. Am. Chem. Soc. , 2002, 124, 1269-1275
Assembled by п-п interaction
Temperature-dependent CD (a), UV/vis (b), and fluorescence (c) spectra of 1 in nbutanol (2.6*10-5 mol.L-1). The last: Temperature-dependent CD spectra of 1 in water
28
A. P. H. J. Schenning, E. W. Meijer, J. Am. Chem. Soc. , 2002, 124, 1269-1275
Assembled by п-п interaction
The chirality of the monomers’ side chains imparts chirality to the aggregates
a) AFM phase image showing the preferential orientation of large ribbons on graphite.
b) STM topographic image showing the internal structure of a large ribbon on graphite.
c) AFM phase image on silicon, showing left-handed helical aggregates.
29
A. P. H. J. Schenning, E. W. Meijer, J. Am. Chem. Soc. , 2002, 124, 1269-1275
Assembled by п-п interaction
Ph. Leclere, E.W. Meijer, European Polymer Journal, 2004, 40, 885–892
30
Assembled by п-п interaction
Ph. Leclere, E.W. Meijer, European Polymer Journal, 2004, 40, 885–892
31
Assembled by п-п interaction
AFM image of a thin deposit on mica
of (a) 1a from THF; (b) 1b from THF;
(c) 1c from THF; (d) 1d from toluene.
The scale bar represents 500 nm.
Ph. Leclere, E.W. Meijer, European Polymer Journal, 2004, 40, 885–892
32
Assembled by п-п interaction
AFM images of conjugated chiral oligomers
deposited on Si/SiOx: (a) 2a from toluene;
(b) 2c from toluene; (c) and (d) 4c from
THF. The scale bar represents 1.0 nm.
1) Polarity of the silicon plays
an important role in the
expression of chirality
2) Thermodynamic and kinetic
control are also important
Ph. Leclere, E.W. Meijer, European Polymer Journal, 2004, 40, 885–892
33
Assembled by п-п interaction
AFM images of: (a) 2a on graphite;
(b) 2a on mica; (c) 3a on Si/SiOx;
and (d) 3b on graphite.
The scale bar represents 1.0 um.
Ph. Leclere, E.W. Meijer, European Polymer Journal, 2004, 40, 885–892
34
Assembled by п-п interaction
Molecular structure of the oligo(p-phenylenevinylene) derivatives OPV-x [for
OPV-3, y =1; OPV-4, y=2; and OPV-5, y=3] and schematic representation of the
self-assembly process.
35
Pascal Jonkheijm, E. W. Meijer, Science, 2006, 313, 80
Assembled by п-п interaction
STM images of dimeric OPV4 monolayers
on graphite(A) Image size is 12.1*12.1 nm2
(B) Molecular model representing the 2D
ordering in A.
STM image of mixed lamellae of
OPV3 and OPV4 on a graphite
surface from a concentrated 1,2,4trichlorobenzene solution.
36
A. Gesquiere, E. W. Meijer, Nano Lett., 2004, 4, 1175-1179
Assembled by п-п interaction
Tapping mode AFM images (5*5um2) of OPV4 on substrates
drop cast from heptane solutions (6.7*10-6 M) on graphite
37
Pascal Jonkheijm, E. W. Meijer, J. Am. Chem. Soc., 2003, 125, 15949
Assembled by п-п interaction
(D to F) Tapping-mode AFM images of self-assemblies of OPV-4 on graphite surfaces
showing different degree of clustering depending on the concentration of the drop cast
solution
38
Pascal Jonkheijm, E. W. Meijer, J. Am. Chem. Soc., 2003, 125, 15949
Assembled by п-п interaction
Temperature
Polarity of solvent
Symmetry of molecules
Thermodynamic conditions
39
Pascal Jonkheijm, E. W. Meijer, J. Am. Chem. Soc., 2003, 125, 15949
Assembled by п-п interaction
Variable temperature measurements (heating ramp, steps of 10 K) (a) UV/vis
(b) fluorescence and (c) CD spectra for OPV-4 in dodecane solution (14 μM).
40
Pascal Jonkheijm, E. W. Meijer, Science, 2006, 313, 80
Assembled by п-п interaction
41
Pascal Jonkheijm, E. W. Meijer, Science, 2006, 313, 80
Assembled by п-п interaction
This opens the way to align these stacks so as to
connect their ends to electrodes and study the
electro-optical properties of these nanosized
wires.
Ph. Leclere, E.W. Meijer, European Polymer Journal, 2004, 40, 885–892
42
Outline
Introduction
 Lessons from nature
 Scientists’ efforts

Assembled by hydrogen bond
Assembled by п-п interaction
Assembled by metal-ligand
Scientists’ bionic results
Conclusion and outlook
 Acknowledgement

43
Assembled by metal-ligand
1) High rational design predictability by simple variation of
the size and shape of the building units.
2) Large number and diversity of possible transition metal
complexes.
3) Bond energies in the range of 15 ± 30 kcal.mol-1 per
interaction that fall between those of the strong covalent
bonds in classical macrocycles and the weak interactions.
4) Excellent product yields inherent in the self-assembly
process.
44
Assembled by metal-ligand
P. J. Stang, Chem. Eur. J., 1998, 4, 19-27
45
Assembled by metal-ligand
P. J. Stang, Chem. Eur. J., 1998, 4, 19-27
46
Assembled by metal-ligand
Near quantitative yields
P. J. Stang, D. H. Cao, J. Am. Chem. Soc. 1995, 117, 6273
P. J. Stang, J. A. Whiteford, Res. Chem. Intermed. 1996, 22, 659.
47
Assembled by metal-ligand
Crystallographic data (left)
Space-filling models (right)
J. A. Whiteford, C. V. Lu, P. J. Stang, J. Am. Chem. Soc. 1997, 119, 2524
48
Assembled by metal-ligand
49
P. J. Stang, D. H. Cao, J. Am. Chem. Soc. 1997, 119, 5163.
Assembled by metal-ligand
Nanosized cavities.
J. Manna, P. J. Stang, J. Am. Chem. Soc. 1996, 118, 8731.
50
Assembled by metal-ligand
Twelve units come together precisely
with high yield: A Remarkable reaction
P. J. Stang, N. E. Persky, J. Manna, J. Am. Chem. Soc. 1997, 119, 4777.
51
Assembled by metal-ligand
Octahedron by
3-D assembly
P. J. Stang, B. Olenyuk, D. C. Muddiman, Organometallics, 1997, 16, 3094.
52
Assembled by metal-ligand
In fact the real challenges, as in all of contemporary
supramolecular chemistry, are the proper characterization and
structure determination of the species observed. This challenge
increases with the complexity of the supramolecular species, from
simple polygons (triangles and squares) to complex polyhedra
(cuboctahedron, dodecahedron, etc.).
P. J. Stang 1998
53
Assembled by metal-ligand
Molecular modeling:
D=3.7 nm
i) N-ethylmorpholine, MeOH, 12 h, reflux; b) methanolic NH4PF6
George R. Newkome, Tae Joon Cho, Chem. Eur. J. 2002, 8, 2946-2954
54
Assembled by metal-ligand
Transmission electron micrograph of 18+12.12PF6 (magnification of
200000) showing an individual, regular hexagon.
George R. Newkome, Tae Joon Cho, Chem. Eur. J. 2002, 8, 2946-2954
55
Assembled by metal-ligand
Sierpinski’s hexagonal
gasket synthesized by
Newkome
Energy minimization calculations
12.3 nm in diameter and 0.7 nm in height
George R. Newkome, Pingshan Wang, et al., Science, 2006, 312, 1783
56
Assembled by metal-ligand
Synthetic route:
(a) 1 and 2 were mixed with N-ethylmorpholine in refluxing CH3OH/CHCl3
(2:1 v/v), for 20 hours.
(b) 3 and 4 were stirred in refluxing CH3OH with added N-ethylmorpholine
for 12 hours.
57
Assembled by metal-ligand
Synthetic route:
c
(c) First, hexamer 5 was refluxed in CH3OH in the presence of 1 equiv. of
FeCl2.6H2O for 20 hours. Then, to a CH3OH solution of 5(Cl– )m(NO3–)n was
added a solution of NH4PF6 to obtain the desired gasket 6 as a precipitate.
58
Assembled by metal-ligand
Full characterization of hexagonal gasket molecule :
H1NMR: 9.45 ppm attributed to the tpy-Fe-tpy complex and the other at 9.20 ppm
attributed to the tpy-Ru-tpy complex, displaying the requisite1:6 integration.
UV-vis: the absorbance pattern at 575 and 495 nm with a 1:6 ratio for the tpy-Fetpy and tpy-Ru-tpy units, respectively.
MALDI-TOF MS: failed to provide definitive structural information due to
overall 84+ molecular charge.
59
Assembled by metal-ligand
AFM, TEM, UHV-STM
60
Outline
Introduction
 Lessons from nature
 Scientists’ efforts

Assembled by hydrogen bond
Assembled by п-п interaction
Assembled by metal-ligand
Scientists’ bionic results
Conclusion and outlook
 Acknowledgement

61
Scientists’ bionic results
Nucleotide-Appended Thymine (T)
Adenine Nucleotide (A) )
R. Iwaura, E. W. Meijer, T. Shimizu, J. Am. Chem. Soc. 2006, 128, 13298-13304
62
Scientists’ bionic results
R. Iwaura, E. W. Meijer, T. Shimizu, J. Am. Chem. Soc. 2006, 128, 13298-13304
63
Scientists’ bionic results
Right-handed DNA-like nanofibers
Right: (a, b) AFM images for the binary selfassembly from of (T:A=2:1, 1.8*10-2 M/9*10-4 M).
Left: (a,b,c) AFM images for the binary selfassembly of (T:A=1:1 ), 1.8*10-2 M/1.8*10-3 M).
R. Iwaura, E. W. Meijer, T. Shimizu, J. Am. Chem. Soc. 2006, 128, 13298-13304
64
Conclusion and outlook
Design
Model
Lab result
Characterization
Application
65
Conclusion and outlook
Plastic transitors, photovoltaics, molecular machine,
nano-devices
Bionic system
Biosystem…
66
Acknowledgement
Prof. Jian Pei, Prof. Yuguo Ma, Prof. Dahui Zhao
Other professors in Organic Institute
All members in our lab
67
Thanks for your attention !
68